pax_global_header00006660000000000000000000000064140012423040014500gustar00rootroot0000000000000052 comment=c7e349af93302af30e15aa4e65dfdf89d52c32cd bio-vcf-0.9.5/000077500000000000000000000000001400124230400130405ustar00rootroot00000000000000bio-vcf-0.9.5/.gitignore000066400000000000000000000002331400124230400150260ustar00rootroot00000000000000file.vcf Gemfile.lock notes.txt .bundle vendor/ orig/ pkg/ scripts/timings.sh TAGS test/data/regression/*.new data/ fedor.txt test.vcf out.bed rdoc/ *.gem bio-vcf-0.9.5/.travis.yml000066400000000000000000000000341400124230400151460ustar00rootroot00000000000000language: ruby arch: arm64 bio-vcf-0.9.5/Gemfile000066400000000000000000000001461400124230400143340ustar00rootroot00000000000000source "http://rubygems.org" group :development do gem "rake" gem "rspec" gem "cucumber" end bio-vcf-0.9.5/LICENSE.txt000066400000000000000000000021001400124230400146540ustar00rootroot00000000000000Copyright (c) 2013-2020 Pjotr Prins Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. bio-vcf-0.9.5/README.md000066400000000000000000001152161400124230400143250ustar00rootroot00000000000000# bio-vcf [![Build Status](https://secure.travis-ci.org/vcflib/bio-vcf.png)](http://travis-ci.org/vcflib/bio-vcf) [![rubygem](https://img.shields.io/gem/v/bio-vcf.svg?style=flat)](http://rubygems.org/gems/bio-vcf "Install with Rubygems") [![AnacondaBadge](https://anaconda.org/bioconda/bio-vcf/badges/installer/conda.svg)](https://anaconda.org/bioconda/bio-vcf) [![DL](https://anaconda.org/bioconda/bio-vcf/badges/downloads.svg)](https://anaconda.org/bioconda/bio-vcf) [![DebianBadge](https://badges.debian.net/badges/debian/testing/bio-vcf/version.svg)](https://packages.debian.org/testing/bio-vcf) Quick index: - [INSTALL](#Install) - [Command line interface (CLI)](#command-line-interface-cli) + [Set analysis](#set-analysis) + [Genotype processing](#genotype-processing) + [Sample counting](#sample-counting) + [Filter with lambda](#reorder-filter-with-lambda) + [Modify VCF files](#modify-vcf-files) + [RDF output](#rdf-output) - [Templates](#templates) - [Metadata](#metadata) - [Statistics](#statistics) - [API](#api) - [Cite](#cite) ## Bio-vcf Bio-vcf provides a domain specific language (DSL) for processing the VCF format. Record named fields can be queried with regular expressions, e.g. ```ruby sample.dp>20 and rec.filter !~ /LowQD/ and rec.tumor.bcount[rec.alt]>4 ``` Bio-vcf is a new generation VCF parser, filter and converter. Bio-vcf is not only very fast for genome-wide (WGS) data, it also comes with a really nice filtering, evaluation and rewrite language and it can output any type of textual data, including VCF header and contents in RDF and JSON. So, why would you use bio-vcf over other parsers? Because 1. Bio-vcf is fast and scales on multi-core computers 2. Bio-vcf has an expressive filtering and evaluation language 3. Bio-vcf has great multi-sample support 4. Bio-vcf has multiple global filters and sample filters 5. Bio-vcf can access any VCF format 6. Bio-vcf can parse and query the VCF header (META data) 7. Bio-vcf can do calculations on fields 8. Bio-vcf allows for genotype processing 9. Bio-vcf has support for set analysis 10. Bio-vcf has sane error handling 11. Bio-vcf can convert *any* VCF to *any* output, including tabular data, BED, HTML, LaTeX, RDF, JSON and JSON-LD and even other VCFs by using (erb) templates 12. Bio-vcf has soft filters Some examples are documented for [reducing GTeX](doc/GTEx_reduce.md), [comparing GATK](doc/GATK_comparison.md), [comparing VCFs](doc/Compare_VCFs.md), JSON [loading Mongo database](doc/Using_Mongo.md), and [generating RDF](doc/Using_RDF.md). ## Options In true Unix fashion files can be piped in or passed on the command line: bio-vcf --help ``` bio-vcf (biogem with pcows) by Pjotr Prins 2015-2020 Usage: bio-vcf [options] filename e.g. bio-vcf < test/data/input/somaticsniper.vcf -i, --ignore-missing Ignore missing data --filter cmd Evaluate filter on each record --sfilter cmd Evaluate filter on each sample --sfilter-samples list Filter on selected samples (e.g., 0,1 --ifilter, --if cmd Include filter --ifilter-samples list Include set - implicitely defines exclude set --efilter, --ef cmd Exclude filter --efilter-samples list Exclude set - overrides exclude set --add-filter name Set/add filter field to name --bed bedfile Filter on BED elements -e, --eval cmd Evaluate command on each record --eval-once cmd Evaluate command once (usually for header info) --seval cmd Evaluate command on each sample --rewrite eval Rewrite INFO --samples list Output selected samples --rdf Generate Turtle RDF (also check out --template!) --num-threads [num] Multi-core version (default ALL) --thread-lines num Fork thread on num lines (default 40000) --skip-header Do not output VCF header info --set-header list Set a special tab delimited output header (#samples expands to sample names) -t, --template erb Use ERB template for output --add-header-tag Add bio-vcf status tag to header output --timeout [num] Timeout waiting for thread to complete (default 180) --names Output sample names --statistics Output statistics -q, --quiet Run quietly -v, --verbose Run verbosely --debug Show debug messages and keep intermediate output --id name Identifier --tags list Add tags -h, --help display this help and exit ``` ## Performance Bio-vcf has better performance than other tools because of lazy parsing, multi-threading, and useful combinations of (fancy) command line filtering. Adding cores, bio-vcf just does better. The more complicated the filters, the larger the gain. First a base line test to show IO performance ```sh time cat ESP6500SI-V2-SSA137.GRCh38-liftover.*.vcf|wc 1987143 15897724 1003214613 real 0m7.823s user 0m7.002s sys 0m2.972s ``` Next run this 1Gb data with bio-vcf effectively using 5 cores on AMD Opteron(tm) Processor 6174 using Linux ```sh time cat ESP6500SI-V2-SSA137.GRCh38-liftover.*.vcf|./bin/bio-vcf -iv --num-threads 8 --filter 'r.info.cp.to_f>0.3' > /dev/null real 0m32.491s user 2m34.767s sys 0m12.733s ``` The same with SnpSift v4.0 takes ```sh time cat ESP6500SI-V2-SSA137.GRCh38-liftover.*.vcf|java -jar snpEff/SnpSift.jar filter "( CP>0.3 )" > /dev/null real 12m36.121s user 12m53.273s sys 0m9.913s ``` This means that on this machine bio-vcf is 24x faster than SnpSift even for a simple filter. In fact, bio-vcf is perfect for complex filters and parsing large data files on powerful machines. Parsing a 650 Mb GATK Illumina Hiseq VCF file and evaluating the results into a BED format on a 16 core machine takes ```sh time bio-vcf --num-threads 16 --filter 'r.chrom.to_i>0 and r.chrom.to_i<21 and r.qual>50' --sfilter '!s.empty? and s.dp>20' --eval '[r.chrom,r.pos,r.pos+1]' < test.large2.vcf > test.out.3 real 0m47.612s user 8m18.234s sys 0m5.039s ``` which shows decent core utilisation (10x). Running gzip compressed VCF files of 30+ Gb has similar performance gains. To view some complex filters on an 80Gb SNP file check out a [GTEx exercise](https://github.com/vcflib/bio-vcf/blob/master/doc/GTEx_reduce.md). Use zcat (or even better pigz which is multi-core itself) to pipe such gzipped (vcf.gz) files into bio-vcf, e.g. ```sh zcat huge_file.vcf.gz| bio-vcf --num-threads 36 --filter 'r.chrom.to_i>0 and r.chrom.to_i<21 and r.qual>50' --sfilter '!s.empty? and s.dp>20' --eval '[r.chrom,r.pos,r.pos+1]' > test.bed ``` bio-vcf comes with a sensible parser definition language, an embedded Ragel parser for INFO and FORMAT header definitions, as well as primitives for set analysis. Few assumptions are made about the actual contents of the VCF file (field names are resolved on the fly), so bio-vcf should work with all VCF files. To fetch all entries where all samples have depth larger than 20 and filter set to PASS use a sample filter ```ruby bio-vcf --sfilter 'sample.dp>20 and rec.filter=="PASS"' < file.vcf ``` or with a regex ```ruby bio-vcf --sfilter 'sample.dp>20 and rec.filter !~ /LowQD/' < file.vcf ``` To only filter on some samples number 0 and 3: ```ruby bio-vcf --sfilter-samples 0,3 --sfilter 's.dp>20' < file.vcf ``` Where 's.dp' is the shorter name for 'sample.dp'. It is also possible to specify sample names, or info fields: For example, to filter somatic data ```ruby bio-vcf --filter 'rec.info.dp>5 and rec.alt.size==1 and rec.tumor.bq[rec.alt]>30 and rec.tumor.mq>20' < file.vcf ``` To output specific fields in tabular (and HTML, XML or LaTeX) format use the --eval switch, e.g., ```ruby bio-vcf --eval 'rec.alt+"\t"+rec.info.dp+"\t"+rec.tumor.gq.to_s' < file.vcf ``` In fact, if the result is an Array the output gets tab dilimited, so the nicer version is ```ruby bio-vcf --eval '[r.alt,r.info.dp,r.tumor.gq.to_s]' < file.vcf ``` To output the DP values of every sample that has a depth larger than 100: ```ruby bio-vcf -i --sfilter 's.dp>100' --seval 's.dp' < file.vcf 1 10257 159 242 249 249 186 212 218 1 10291 165 249 249 247 161 163 189 1 10297 182 246 250 246 165 158 183 1 10303 198 247 248 248 172 157 182 (etc.) ``` Where -i ignores missing samples. Pick up sample allele depth ```ruby bio-vcf -i --seval 's.ad.to_s' 1 10257 [151, 8] [219, 22] [227, 22] [226, 22] [166, 18] [185, 27] [201, 15] 1 10291 [145, 16] [218, 26] [214, 30] [213, 32] [122, 36] [131, 27] [156, 31] 1 10297 [155, 18] [218, 23] [219, 26] [207, 30] [137, 20] [124, 27] [151, 27] 1 10303 [169, 25] [211, 31] [214, 28] [214, 32] [146, 17] [123, 23] [156, 22] ``` To get the alt depth per sample ```ruby bio-vcf -i --seval 's.ad[1]' 1 10257 8 22 22 22 18 27 15 1 10291 16 26 30 32 36 27 31 1 10297 18 23 26 30 20 27 27 1 10303 25 31 28 32 17 23 22 ``` To calculate percentage non-reference (PNR) alt frequencies from s.ad which is sample (alt dp)/(ref dp + alt dp) ```ruby bio-vcf -i --seval 's.ad[1].to_f/(s.ad[0]+s.ad[1])' 1 10257 0.050314465408805034 0.0912863070539419 0.08835341365461848 0.088709677419354840.09782608695652174 0.12735849056603774 0.06944444444444445 1 10291 0.09937888198757763 0.10655737704918032 0.12295081967213115 0.1306122448979592 0.22784810126582278 0.17088607594936708 0.1657754010695187 ``` note the floating point conversion .to_f is needed, otherwise you get an integer division. To account for multiple alleles ```ruby bio-vcf -i --eval 'r.ref+">"+r.alt[0]' --seval 'tot=s.ad.reduce(:+) ; (tot-s.ad[0].to_f)/tot' --set-header "mutation,#samples" mutation Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 A>C 0.050314465408805034 0.0912863070539419 0.08835341365461848 0.08870967741935484 0.09782608695652174 0.12735849056603774 0.06944444444444445 C>T 0.09937888198757763 0.10655737704918032 0.12295081967213115 0.1306122448979592 0.22784810126582278 0.17088607594936708 0.1657754010695187 ``` To output DP ang GQ values for tumor normal: ```ruby bio-vcf --filter 'r.normal.dp>=7 and r.tumor.dp>=5' --seval '[s.dp,s.gq]' < freebayes.vcf 17 45235620 22 139.35 20 0 17 45235635 20 137.224 14 41.5688 17 45235653 18 146.509 12 146.509 17 45247354 32 0 9 6.59312 17 45247362 27 0 6 110.097 ``` To parse and output genotype ```ruby bio-vcf -iq --sfilter 's.dp>=20 and s.gq>=20' --ifilter-samples 's.gt!="0/0"' --seval s.gt < test/data/input/multisample.vcf 1 10257 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1 10291 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1 10297 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1 12783 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ``` And use --set-header if you want to add a header ```ruby bio-vcf -iq --set-header 'chr,pos,#samples' --sfilter 's.dp>=20 and s.gq>=20' --ifilter-samples 's.gt!="0/0"' --seval s.gt < test/data/input/multisample.vcf chr pos orig s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 1 10257 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1 10291 0/1 0/1 0/1 0/1 0/1 0/1 0/1 (etc) ``` where #samples gets expanded. Most filter and eval commands can be used at the same time. Special set commands exit for filtering and eval. When a set is defined, based on the sample name, you can apply filters on the samples inside the set, outside the set and over all samples. E.g. So, why would you use bio-vcf instead of rolling out your own Perl/Python/other ad-hoc script? I think the reason should be that there is less chance of mistakes because of Bio-vcf's clear filtering language and sensible built-in validation. The second reason would be speed. Bio-vcf's multi-threading capability gives it great and hard to replicate performance. Also note you can use [bio-table](https://github.com/pjotrp/bioruby-table) to filter/transform data further and convert to other formats, such as RDF. The VCF format is commonly used for variant calling between NGS samples. The fast parser needs to carry some state, recorded for each file in VcfHeader, which contains the VCF file header. Individual lines (variant calls) first go through a raw parser returning an array of fields. Further (lazy) parsing is handled through VcfRecord. At this point the filter is pretty generic with multi-sample support. If something is not working, check out the feature descriptions and the source code. It is not hard to add features. Otherwise, send a short example of a VCF statement you need to work on. ## Install Requirements: * ruby To install bio-vcf with Ruby gems, install Ruby first, e.g. on Debian (as root) ```sh apt-get install ruby ``` Installing ruby includes the `gem` command to install bio-vcf: ```sh gem install bio-vcf export PATH=/usr/local/bin:$PATH bio-vcf -h ``` displays the help ``` bio-vcf x.x (biogem Ruby with pcows) by Pjotr Prins 2015-2020 Usage: bio-vcf [options] filename e.g. bio-vcf < test/data/input/somaticsniper.vcf -i, --ignore-missing Ignore missing data --filter cmd Evaluate filter on each record (etc.) ``` To install without root you may install a gem locally with ```sh gem install --install-dir ~/bio-vcf bio-vcf ``` and run it with something like ```sh ~/bio-vcf/gems/bio-vcf-0.9.4/bin/bio-vcf -h ``` Finally, it is possible to checkout the git repository and simply run the tool with ```sh git clone https://github.com/vcflib/bio-vcf.git cd bio-vcf ruby ./bin/bio-vcf -h ``` ## Command line interface (CLI) Get the version of the VCF file ```ruby bio-vcf -q --eval-once header.version < file.vcf 4.1 ``` Get the column headers ```ruby bio-vcf -q --eval-once 'header.column_names.join(",")' < file.vcf CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT,NORMAL,TUMOR ``` Get the sample names ```ruby bio-vcf -q --eval-once 'header.samples.join(",")' < file.vcf NORMAL,TUMOR ``` Alternatively use the command line switch for --names, e.g. ```ruby bio-vcf --names < file.vcf NORMAL,TUMOR ``` Get information from the header (META) ```ruby bio-vcf -q --skip-header --eval-once 'header.meta["GATKCommandLine"]' < gatk_exome.vcf ``` The 'fields' array contains unprocessed data (strings). Print first five raw fields ```ruby bio-vcf --eval 'fields[0..4]' < file.vcf ``` Add a filter to display the fields on chromosome 12 ```ruby bio-vcf --filter 'fields[0]=="12"' --eval 'fields[0..4]' < file.vcf ``` It gets better when we start using processed data, represented by an object named 'rec'. Position is a value, so we can filter a range ```ruby bio-vcf --filter 'rec.chrom=="12" and rec.pos>96_641_270 and rec.pos<96_641_276' < file.vcf ``` The shorter name for 'rec.chrom' is 'r.chrom', so you may write ```ruby bio-vcf --filter 'r.chrom=="12" and r.pos>96_641_270 and r.pos<96_641_276' < file.vcf ``` To ignore and continue parsing on missing data use the --ignore-missing (-i) and or --quiet (-q) switches ```ruby bio-vcf -i --filter 'r.chrom=="12" and r.pos>96_641_270 and r.pos<96_641_276' < file.vcf ``` Info fields are referenced by ```ruby bio-vcf --filter 'rec.info.dp>100 and rec.info.readposranksum<=0.815' < file.vcf ``` (alternatively you can use the indexed rec.info['DP'] and list INFO fields with rec.info.fields). Subfields defined by rec.format: ```ruby bio-vcf --filter 'rec.tumor.ss != 2' < file.vcf ``` Output ```ruby bio-vcf --filter 'rec.tumor.gq>30' --eval '[rec.ref,rec.alt,rec.tumor.bcount,rec.tumor.gq,rec.normal.gq]' < file.vcf ``` Show the count of the bases that were scored as somatic ```ruby bio-vcf --eval 'rec.alt+"\t"+rec.tumor.bcount.split(",")[["A","C","G","T"].index(rec.alt)]+ "\t"+rec.tumor.gq.to_s' < file.vcf ``` Actually, we have a convenience implementation for bcount, so this is the same ```ruby bio-vcf --eval 'rec.alt+"\t"+rec.tumor.bcount[rec.alt].to_s+"\t"+rec.tumor.gq.to_s' < file.vcf ``` Filter on the somatic results that were scored at least 4 times ```ruby bio-vcf --filter 'rec.alt.size==1 and rec.tumor.bcount[rec.alt]>4' < test.vcf ``` Similar for base quality scores ```ruby bio-vcf --filter 'rec.alt.size==1 and rec.tumor.amq[rec.alt]>30' < test.vcf ``` Filter out on sample values ```ruby bio-vcf --sfilter 's.dp>20' < test.vcf ``` To filter missing on samples: ```sh bio-vcf --filter "rec.s3t2?" < file.vcf ``` or for all ```sh bio-vcf --filter "rec.missing_samples?" < file.vcf ``` To set a soft filter, i.e. the filter column is updated ```sh bio-vcf --add-filter LowQD --filter 'r.tumor.dp<5' < test/data/input/somaticsniper.vcf |bio-vcf --eval '[r.chr,r.pos,r.tumor.dp,r.filter]' --filter 'r.filter.index("LowQD")' ``` may render something like ``` 1 46527674 4 LowQD 1 108417572 4 LowQD 1 155449089 4 LowQD 1 169847826 4 LowQD 1 203098164 3 LowQD 2 39213209 4 LowQD ``` Likewise you can check for record validity ```sh bio-vcf --filter "not rec.valid?" < file.vcf ``` which, at this point, simply counts the number of fields. If your samples have other names you can fetch genotypes for that sample with ```sh bio-vcf --eval "rec.sample['Original'].gt" < file.vcf ``` Or read depth for another ```sh bio-vcf --eval "rec.sample['s3t2'].dp" < file.vcf ``` Better even, you can access samples directly with ```sh bio-vcf --eval "rec.sample.original.gt" < file.vcf bio-vcf --eval "rec.sample.s3t2.dp" < file.vcf ``` And even better because of Ruby magic ```sh bio-vcf --eval "rec.original.gt" < file.vcf bio-vcf --eval "rec.s3t2.dp" < file.vcf ``` Note that only valid method names in lower case get picked up this way. Also by convention normal is sample 1 and tumor is sample 2. Even shorter r is an alias for rec ```sh bio-vcf --eval "r.original.gt" < file.vcf bio-vcf --eval "r.s3t2.dp" < file.vcf ``` ## Special functions Note: special functions are not yet implemented! Look below for genotype processing which has indexing in 'gti'. Sometime you want to use a special function in a filter. For example percentage variant reads can be defined as [a,c,g,t] with frequencies against sample read depth (dp) as [0,0.03,0.47,0.50]. Filtering would with a special function, which we named freq ```sh bio-vcf --sfilter "s.freq(2)>0.30" < file.vcf ``` which is equal to ```sh bio-vcf --sfilter "s.freq.g>0.30" < file.vcf ``` To check for ref or variant frequencies use more sugar ```sh bio-vcf --sfilter "s.freq.var>0.30 and s.freq.ref<0.10" < file.vcf ``` For all includes var should be identical for set analysis except for cartesian. So when --include is defined test for identical var and in the case of cartesian one unique var, when tested. ref should always be identical across samples. ## DbSNP One clinical variant DbSNP example ```sh bio-vcf --eval '[rec.id,rec.chr,rec.pos,rec.alt,rec.info.sao,rec.info.CLNDBN]' < clinvar_20140303.vcf ``` renders ``` 1 1916905 rs267598254 A 3 Malignant_melanoma 1 1916906 rs267598255 A 3 Malignant_melanoma 1 1959075 rs121434580 C 1 Generalized_epilepsy_with_febrile_seizures_plus_type_5 1 1959699 rs41307846 A 1 Generalized_epilepsy_with_febrile_seizures_plus_type_5|Epilepsy\x2c_juvenile_myoclonic_7|Epilepsy\x2c_idiopathic_generalized_10 1 1961453 rs142619552 T 3 Malignant_melanoma 1 2160299 rs387907304 G 0 Shprintzen-Goldberg_syndrome 1 2160305 rs387907306 A T 0 Shprintzen-Goldberg_syndrome,Shprintzen-Goldberg_syndrome 1 2160306 rs387907305 A T 0 Shprintzen-Goldberg_syndrome,Shprintzen-Goldberg_syndrome 1 2160308 rs397514590 T 0 Shprintzen-Goldberg_syndrome 1 2160309 rs397514589 A 0 Shprintzen-Goldberg_syndrome ``` ## Set analysis bio-vcf allows for set analysis. With the complement filter, for example, samples are selected that evaluate to true, all others should evaluate to false. For this we create three filters, one for all samples that are included (the --ifilter or -if), for all samples that are excluded (the --efilter or -ef) and for any sample (the --sfilter or -sf). So i=include (OR filter), e=exclude and s=any sample (AND filter). The equivalent of the union filter is by using the --sfilter, so ```sh bio-vcf --sfilter 's.dp>20' ``` Filters DP on all samples and is true if all samples match the criterium (AND). To filter on a subset you can add a selector ```sh bio-vcf --sfilter-samples 0,1,4 --sfilter 's.dp>20' ``` For set analysis there are the additional ifilter (include) and efilter (exclude). Where sfilter represents an ALL match, the ifilter represents an ANY match, i.e., it is true if one of the samples matches the criterium (OR). To filter on samples 0,1,4 and output the gq values ```sh bio-vcf -i --ifilter-samples 0,1,4 --ifilter 's.gq<10 or s.gq==99' --seval s.gq 1 14907 99 99 99 99 99 99 99 1 14930 99 99 99 99 99 99 99 1 14933 1 99 99 39 99 99 99 1 15190 99 99 91 99 99 99 99 1 15211 99 99 99 99 99 99 99 ``` The equivalent of the complement filter is by specifying what samples to include, here with a regex and define filters on the included and excluded samples (the ones not in ifilter-samples) and the ```sh ./bin/bio-vcf -i --sfilter 's.dp>20' --ifilter-samples 2,4 --ifilter 's.gt==r.s1t1.gt' ``` To print out the GT's add --seval ```sh bio-vcf -i --sfilter 's.dp>20' --ifilter-samples 2,4 --ifilter 's.gt==r.s1t1.gt' --seval 's.gt' 1 14673 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1 14907 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1 14930 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1 15211 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1 15274 1/2 1/2 1/2 1/2 1/2 1/2 1/2 1 16103 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ``` To set an additional filter on the excluded samples: ```sh bio-vcf -i --ifilter-samples 0,1,4 --ifilter 's.gt==rec.s1t1.gt and s.gq>10' --seval s.gq --efilter 's.gq==99' ``` Etc. etc. Any combination of sfilter, ifilter and efilter is possible. Currently the efilter is an ALL filter (AND), i.e. all excluded samples need to match the criterium. The following regular expression matches are not yet implemented: In the near future it is also possible to select samples on a regex (here select all samples where the name starts with s3) ```sh bio-vcf --isample-regex '/^s3/' --ifilter 's.dp>20' ``` ```sh bio-vcf --include /s3.+/ --sfilter 'dp>20' --ifilter 'gt==s3t1.gt' --efilter 'gt!=s3t1.gt' --set-intersect include=true bio-vcf --include /s3.+/ --sample-regex /^t2/ --sfilter 'dp>20' --ifilter 'gt==s3t1.gt' --set-catesian one in include=true, rest=false bio-vcf --unique-sample (any) --include /s3.+/ --sfilter 'dp>20' --ifilter 'gt!="0/0"' ``` With the filter commands you can use --ignore-missing to skip errors. ## Genotype processing The sample GT field counts 0 as the reference and numbers >1 as indexed ALT values. The field is simply built up using a slash or | as a separator (e.g., 0/1, 0|2, ./. are valid values). The standard field results in a string value ```ruby bio-vcf --seval s.gt 1 10665 ./. ./. 0/1 0/1 ./. 0/0 0/0 1 10694 ./. ./. 1/1 1/1 ./. ./. ./. 1 12783 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1 15274 1/2 1/2 1/2 1/2 1/2 1/2 1/2 ``` to access components of the genotype field we can use standard Ruby ```ruby bio-vcf --seval 's.gt.split(/\//)[0]' 1 10665 . . 0 0 . 0 0 1 10694 . . 1 1 . . . 1 12783 0 0 0 0 0 0 0 1 15274 1 1 1 1 1 1 1 ``` or special functions, such as 'gti' which gives the genotype as an indexed value array ```ruby bio-vcf --seval 's.gti[0]' 1 10665 0 0 0 0 1 10694 1 1 1 12783 0 0 0 0 0 0 0 1 15274 1 1 1 1 1 1 1 ``` and 'gts' as a nucleotide string array ```ruby bio-vcf --seval 's.gts' 1 10665 C C C C 1 10694 G G 1 12783 G G G G G G G 1 15274 G G G G G G G ``` where gts represents the indexed genotype on [ref] + [alt]. To convert combined genotypes into numbers, i.e., 0/0 -> 0, 0/1 -> 1, 1/1 -> 2, is useful for indexed fields giving information on, for example signficance, use ```ruby bio-vcf --seval '!s.empty? and s.gtindex' 11 58949455 0 1 11 65481082 0 1 11 94180424 0 1 11 121036021 0 1 ``` Now you can index other fields, e.g. GL ```ruby ./bin/bio-vcf --seval '[(!s.empty? ? s.gl[s.gtindex]:-1)]' 1 900057 1.0 1.0 0.994 1.0 1.0 -1 0.999 1.0 0.997 -1 0.994 0.989 -1 0.991 -1 0.972 0.992 1.0 ``` shows a number of SNPs have been scored with high significance and a number are missing, here marked as -1. These values can also be used in filters and output allele depth, for example ```ruby bio-vcf -vi --ifilter 'rec.original.gt!="0/1"' --efilter 'rec.original.gt=="0/0"' --seval 'rec.original.ad[s.gti[1]]' 1 10257 151 151 151 151 151 8 151 1 13302 26 10 10 10 10 10 10 1 13757 47 47 4 47 47 4 47 ``` You can use the genotype index gti to fetch values from, for example, allele depth: ```ruby bio-vcf -vi --ifilter 'rec.original.gt!="0/1"' --efilter 'rec.original.gti[0]==0' --seval 'rec.original.ad[s.gti[1]]' 1 10257 151 151 151 151 151 8 151 1 13302 26 10 10 10 10 10 10 1 13757 47 47 4 47 47 4 47 ``` ## Sample counting Note, the use of lambda allows for sophisticated queries. You may need some expert advice here. To count valid genotype field in samples you can do something like ```ruby bio-vcf --eval 'r.samples.count {|s| s.gt!="./."}' ``` A similar complex count would be ```ruby bio-vcf --eval '[r.chr,r.pos,r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }]' ``` which tests for perfect SNPs scored (for example). ## Reorder filter with lambda Sometime it pay to reorder the filter using a lambda. This is one example where the greedy sample counts are done only for those samples that match the other criteria: ```ruby ./bin/bio-vcf --num-threads=1 --filter '(r.info.miss<0.05 and r.info.exp_freq_a1>0.05 and r.info.exp_freq_a1<0.95 and r.info.impinfo>0.7 and r.info.hw<1.0) ? lambda { found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; found/total>0.7 and total-found<30 }.call : false)' ``` ## Modify VCF files Add or modify the sample file name in the INFO fields: ```sh bio-vcf --rewrite 'rec.info["sample"]="mytest"' < mytest.vcf ``` To remove/select 3 samples: ```sh bio-vcf --samples 0,1,3 < mytest.vcf ``` You can also select samples by name (as long as they do not contain spaces) ```sh bio-vcf --names < mytest.vcf Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 bio-vcf --samples "Original,s1t1,s3t1" < mytest.vcf ``` Filter on a BED file and annotate the gene name in the resulting VCF ```sh bio-vcf -v --bed test/data/input/test.bed --rewrite 'rec.info["gene"]=bed[3]' < test/data/input/somaticsniper.vcf ``` ## RDF output You can use --rdf for turtle RDF output from simple one-liners, note the use of --id and --tags which includes the MAF record: ```ruby bio-vcf --id evs --rdf --tags '{"db:evs" => true, "seq:freq" => rec.info.maf[0]/100 }' < EVS.vcf :evs_ch9_139266496_T seq:chr "9" . :evs_ch9_139266496_T seq:pos 139266496 . :evs_ch9_139266496_T seq:alt T . :evs_ch9_139266496_T db:vcf true . :evs_ch9_139266496_T db:evs true . :evs_ch9_139266496_T seq:freq 0.419801 . ``` Also check out the more powerful templating system below. It is possible to filter too! Pick out the rare variants with ```ruby bio-vcf --id evs --filter 'r.info.maf[0]<5.0' --rdf --tags '{"db:evs" => true, "seq:freq" => rec.info.maf[0]/100 }' < EVS.vcf ``` Similarly for GoNL ```ruby bio-vcf --id gonl --rdf --tags '{"db:gonl" => true, "seq:freq" => rec.info.af }' < GoNL.vcf ``` or without AF ```ruby bio-vcf --id gonl --rdf --tags '{"db:gonl" => true, "seq:freq" => (rec.info.ac.to_f/rec.info.an).round(2) }' < gonl_germline_overlap_r4.vcf ``` Also check out [bio-table](https://github.com/pjotrp/bioruby-table) to convert tabular data to RDF. ## Templates To have more output options bio-vcf can use an [ERB template](http://www.stuartellis.eu/articles/erb/) for every match. This is a very flexible option that can output textual formats such as JSON, YAML, HTML and RDF. Examples are provided in [./templates](https://github.com/vcflib/bio-vcf/templates/). A JSON template could be ```Javascript { "seq:chr": "<%= rec.chrom %>" , "seq:pos": <%= rec.pos %> , "seq:ref": "<%= rec.ref %>" , "seq:alt": "<%= rec.alt[0] %>" , "seq:maf": <%= rec.info.maf[0] %> , "dp": <%= rec.info.dp %> }; ``` To get JSON, run with something like (combining with a filter) ```sh bio-vcf --template template/vcf2json.erb --filter 'r.info.sao==1' < dbsnp.vcf ``` which renders ```Javascript { "seq:chr": "13" , "seq:pos": 35745475 , "seq:ref": "C" , "seq:alt": "T" , "seq:maf": 0.0151 , "dp": 86 }; ``` Likewise for RDF output: ```sh bio-vcf --template template/vcf2rdf.erb --filter 'r.info.sao==1' < dbsnp.vcf ``` renders the ERB template ```ruby <% id = Turtle::mangle_identifier(['ch'+rec.chrom,rec.pos,rec.alt.join('')].join('_')) %> :<%= id %> :query_id "<%= id %>", seq:chr "<%= rec.chrom %>" , seq:pos <%= rec.pos %> , seq:ref "<%= rec.ref %>" , seq:alt "<%= rec.alt[0] %>" , seq:maf <%= (rec.info.maf[0]*100).round %> , seq:dp <%= rec.info.dp %> , db:vcf true . ``` into ``` :ch13_33703698_A :query_id "ch13_33703698_A", seq:chr "13" , seq:pos 33703698 , seq:ref "C" , seq:alt "A" , seq:maf 16 , seq:dp 92 , db:vcf true . ``` Note the calculated field value for maf. Be creative! You can write templates for csv, HTML, XML, LaTeX, RDF, JSON, YAML, JSON-LD, etc. etc.! ### Metadata Templates can also print data as a header of the JSON/YAML/RDF output. For this use the '=' prefix with HEADER, BODY, FOOTER keywords in the template. A small example can be ```Javascript =HEADER <% require 'json' %> { "HEADER": { "options": <%= options.to_h.to_json %>, "files": <%= ARGV %>, "version": "<%= BIOVCF_VERSION %>" }, "BODY":[ =BODY { "seq:chr": "<%= rec.chrom %>" , "seq:pos": <%= rec.pos %> , "seq:ref": "<%= rec.ref %>" , "seq:alt": "<%= rec.alt[0] %>" , "dp": <%= rec.info.dp %> }, =FOOTER ] } ``` with ```sh bio-vcf --template template/vcf2json.erb < dbsnp.vcf ``` may generate something like ```Javascript { "HEADER": { "options": {"show_help":false,"source":"https://github.com/CuppenResearch/bioruby-vcf","version":"0.8.1-pre3 (Pjotr Prins)","date":"2014-11-26 12:51:36 +0000","thread_lines":40000,"template":"template/vcf2json.erb","skip_header":true}, "files": [], "version": "0.8.1-pre3" }, "BODY":[ { "seq:chr": "1" , "seq:pos": 883516 , "seq:ref": "G" , "seq:alt": "A" , "dp": }, { "seq:chr": "1" , "seq:pos": 891344 , "seq:ref": "G" , "seq:alt": "A" , "dp": , }, ] } ``` Note that the template is not smart enough to remove the final comma from the last BODY element. To make it valid JSON that needs to be removed. A future version may add a parameter to the BODY element or a global rewrite function for this purpose. YAML and RDF have no such issue. ### Using full VCF header (meta) info To get and put the full information from the header, simple use vcf.meta.to_json. See ./template/vcf2json_full_header.erb for an example. This meta information can also be used to output info fields and sample values on the fly! For an example, see the template at [./template/vcf2json_use_meta.erb](https://github.com/vcflib/bio-vcf/tree/master/template/vcf2json_use_meta.erb) and the generated output at [./test/data/regression/vcf2json_use_meta.ref](https://github.com/vcflib/bio-vcf/tree/master/test/data/regression/vcf2json_use_meta.ref). This way, it is possible to write templates that can convert the content of *any* VCF file without prior knowledge to JSON, RDF, etc. ## Statistics Simple statistics are available for REF>ALT changes: ```sh ./bin/bio-vcf -v --statistics < test/data/input/dbsnp.vcf ``` ## ==== Statistics ================================== G>A 59 45% C>T 30 23% A>G 5 4% C>G 5 4% C>A 5 4% G>T 4 3% T>C 4 3% G>C 4 3% T>A 3 2% A>C 3 2% A>T 2 2% GTCCGACCGCTCC>G 1 1% CGACCGCTCC>C 1 1% T>TGGAGC 1 1% C>CGTCTTCA 1 1% TG>T 1 1% AC>A 1 1% Total 130 ## ================================================== ## Other examples For more exercises and examples see [doc](https://github.com/vcflib/bio-vcf/tree/master/doc) directory and the the feature [section](https://github.com/vcflib/bio-vcf/tree/master/features). ## API BioVcf can also be used as an API. The following code is basically what the command line interface uses (see ./bin/bio-vcf) ```ruby FILE.each_line do | line | if line =~ /^##fileformat=/ # ---- We have a new file header header = VcfHeader.new header.add(line) STDIN.each_line do | headerline | if headerline !~ /^#/ line = headerline break # end of header end header.add(headerline) end end # ---- Parse VCF record line # fields = VcfLine.parse(line,header.columns) fields = VcfLine.parse(line) rec = VcfRecord.new(fields,header) # # Do something with rec # end ``` ### VCFFile The class ```BioVcf::VCFfile``` wraps a file and provides an ```enum``` with the method each, that can be used as in iterator. ```ruby vcf_file = "dbsnp.vcf" vcf = BioVcf::VCFfile.new(file:file, is_gz: false ) it vcf.each puts it.peek vcf_file = "dbsnp.vcf.gz" vcf = BioVcf::VCFfile.new(file:file, is_gz: true ) it vcf.each puts it.peek ``` ## Trouble shooting ### MRI supports threading Note that Ruby 2.x is required for Bio-vcf. JRuby works, but only in single threaded mode (for now). ### Set TMPDIR when running out of space The multi-threading creates temporary files using the system TMPDIR. This behaviour can be overridden by setting the environment variable. ### Reorder filter on time out Make sure to minimize expensive calculations by moving them backward. An 'and' statement is evaluated from left to right. With ```ruby fast_check and slow_check ``` slow_check only gets executed if fast_check is true. For more complex filters use lambda inside a conditional ```ruby ( fast_check ? lambda { slow_check }.call : false ) ``` where slow_check is the slow section of your query. As is shown earlier in this document. Don't forget the .call! ### Reduce thread lines on timeout Depending on your input data and the speed filters it may be useful to tweak the number of thread lines and/or to increase the timeout. On really fast file systems for genome-wide sequencing try increasing --thread-lines to a value larger than 100_000. On the other hand if the computations are intensive (per line) reduce the number of thread-lines (try 10_000 and 1_000). If processes get killed that is the one to try. For larger files set the timeout to 600, or so. --timeout 600. Different values may show different core use on a machine. ### Development To run the tests from source ```sh bundle install --path vendor/bundle bundle exec rake ``` Note: we develop in a GNU Guix environment, see the header of [guix.scm](guix.scm) which does not use bundler. ### Debugging To debug output use '-v --num-threads=1' for generating useful output. Also do not use the -i switch (ignore errors) when there are problems. ### Could not find rake-10.4.2 in any of the sources Remove Gemfile.lock before running other tools. ### Tmpdir contains (old) bio-vcf directories Multi-threaded bio-vcf writes into a temporary directory during processing. When a process gets interrupted for some reason the temporary directory may remain. ## Project home page Information on the source tree, documentation, examples, issues and how to contribute, see http://github.com/vcflib/bio-vcf ## Cite If you use this software, please cite one of * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475) * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080) ## Biogems.info This Biogem is published at (http://biogems.info/index.html#bio-vcf) ## Copyright Copyright (c) 2014-2020 Pjotr Prins. See LICENSE.txt for further details. bio-vcf-0.9.5/RELEASE_NOTES.md000066400000000000000000000016701400124230400154160ustar00rootroot00000000000000## ChangeLog v0.9.5 (20210118) + Improved README and installation instructions + Added guix.scm build and instructions (no need for bundler) + Moved regressiontest into tree ## ChangeLog v0.9.4 (20201222) This is an important maintenance release of bio-vcf: + Rename bioruby-vcf to bio-vcf and migrate project to [vcflib](https://github.com/vcflib/bio-vcf) + Fixed tests to match recent Ruby updates ## Older release notes + Getting ready for a 1.0 release + Released 0.9.2 as a gem + 0.9.1 removed a rare threading bug and cleanup on error + Added support for soft filters (request by Brad Chapman) + The outputter now writes (properly) in parallel with the parser + bio-vcf turns any VCF into JSON with header information, and allows you to pipe that JSON directly into any JSON supporting language, including Python and Javascript! ## Older changes For older changes view the git [log](https://github.com/vcflib/bio-vcf/commits/master). bio-vcf-0.9.5/Rakefile000066400000000000000000000011021400124230400144770ustar00rootroot00000000000000# encoding: utf-8 # require 'rubygems' require 'rake' # require 'cucumber/rake/task' # Cucumber::Rake::Task.new(:features) do |t| # t.cucumber_opts = "--bundler false" # end desc 'Run cucumber' # without bundler task :features do sh 'cucumber features' end task :default => :features task :test => [ :features ] require 'rdoc/task' Rake::RDocTask.new do |rdoc| version = File.exist?('VERSION') ? File.read('VERSION') : "" rdoc.rdoc_dir = 'rdoc' rdoc.title = "bio-vcf #{version}" rdoc.rdoc_files.include('README*') rdoc.rdoc_files.include('lib/**/*.rb') end bio-vcf-0.9.5/VERSION000066400000000000000000000000061400124230400141040ustar00rootroot000000000000000.9.5 bio-vcf-0.9.5/bin/000077500000000000000000000000001400124230400136105ustar00rootroot00000000000000bio-vcf-0.9.5/bin/bio-vcf000077500000000000000000000344161400124230400150730ustar00rootroot00000000000000#!/usr/bin/env ruby # # bio-vcf parser and transformer # Author:: Pjotr Prins # License:: MIT # # Copyright (C) 2014-2020 Pjotr Prins USAGE = "Vcf parser" gempath = File.dirname(File.dirname(__FILE__)) $: << File.join(gempath,'lib') VERSION_FILENAME=File.join(gempath,'VERSION') version = File.new(VERSION_FILENAME).read.chomp require 'bio-vcf' require 'bio-vcf/pcows' require 'optparse' require 'timeout' require 'fileutils' # Uncomment when using the bio-logger # require 'bio-logger' # log = Bio::Log::LoggerPlus.new 'vcf' # log.outputters = Bio::Log::Outputter.stderr # Bio::Log::CLI.logger('stderr') # Bio::Log::CLI.trace('info') options = { show_help: false, source: 'https://github.com/pjotrp/bioruby-vcf', version: version+' (Pjotr Prins)', date: Time.now.to_s, thread_lines: 40_000, timeout: 180 } opts = OptionParser.new do |o| o.banner = "Usage: #{File.basename($0)} [options] filename\ne.g. #{File.basename($0)} < test/data/input/somaticsniper.vcf" o.on('-i','--ignore-missing', 'Ignore missing data') do options[:ignore_missing] = true end o.on('--filter cmd',String, 'Evaluate filter on each record') do |cmd| options[:filter] = cmd end o.on('--sfilter cmd',String, 'Evaluate filter on each sample') do |cmd| options[:sfilter] = cmd end o.on("--sfilter-samples list", Array, "Filter on selected samples (e.g., 0,1") do |l| options[:sfilter_samples] = l end o.on('--ifilter cmd','--if cmd',String, 'Include filter') do |cmd| options[:ifilter] = cmd end o.on("--ifilter-samples list", Array, "Include set - implicitely defines exclude set") do |l| options[:ifilter_samples] = l end o.on('--efilter cmd','--ef cmd',String, 'Exclude filter') do |cmd| options[:efilter] = cmd end o.on("--efilter-samples list", Array, "Exclude set - overrides exclude set") do |l| options[:efilter_samples] = l end o.on('--add-filter name',String, 'Set/add filter field to name') do |name| options[:add_filter] = name end o.on("--bed bedfile", String, "Filter on BED elements") do |bed| options[:bed] = bed end o.on('-e cmd', '--eval cmd',String, 'Evaluate command on each record') do |cmd| options[:eval] = cmd end o.on('--eval-once cmd',String, 'Evaluate command once (usually for header info)') do |cmd| options[:eval_once] = true options[:eval] = cmd # options[:num_threads] = 1 # options[:thread_lines] = 1 options[:skip_header] = true end o.on('--seval cmd',String, 'Evaluate command on each sample') do |cmd| options[:seval] = cmd options[:skip_header] = true end o.on("--rewrite eval", "Rewrite INFO") do |s| options[:rewrite] = s end o.on("--samples list", Array, "Output selected samples") do |l| options[:samples] = l end o.on("--rdf", "Generate Turtle RDF (also check out --template!)") do |b| require 'bio-vcf/vcfrdf' options[:rdf] = true options[:skip_header] = true end o.on("--num-threads [num]", Integer, "Multi-core version (default ALL)") do |i| options[:num_threads] = i end o.on("--thread-lines num", Integer, "Fork thread on num lines (default #{options[:thread_lines]})") do |i| options[:thread_lines] = i end o.on_tail("--id name", String, "Identifier") do |s| options[:id] = s end o.on_tail("--tags list", String, "Add tags") do |s| options[:tags] = s end o.on("--skip-header", "Do not output VCF header info") do options[:skip_header] = true end o.on("--set-header list", Array, "Set a special tab delimited output header (#samples expands to sample names)") do |list| options[:set_header] = list options[:skip_header] = true end o.on("-t erb","--template erb",String, "Use ERB template for output") do |s| require 'bio-vcf/vcfrdf' require 'erb' options[:template] = s options[:skip_header] = true end o.on("--add-header-tag", "Add bio-vcf status tag to header output") do |t| options[:tag] = true end o.on("--timeout [num]", Integer, "Timeout waiting for thread to complete (default #{options[:timeout]})") do |i| options[:timeout] = i end # Uncomment the following when using the bio-logger # o.separator "" # o.on("--logger filename",String,"Log to file (default stderr)") do | name | # Bio::Log::CLI.logger(name) # end # # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s | # Bio::Log::CLI.trace(s) # end # o.on("--names", "Output sample names") do |q| options[:quiet] = true options[:num_threads] = nil options[:eval_once] = true options[:eval] = 'header.samples.join("\t")' # options[:num_threads] = 1 # options[:thread_lines] = 1 options[:skip_header] = true end o.on("--statistics", "Output statistics") do |q| options[:statistics] = true options[:num_threads] = nil end o.on("-q", "--quiet", "Run quietly") do |q| # Bio::Log::CLI.trace('error') options[:quiet] = true end o.on("-v", "--verbose", "Run verbosely") do |v| options[:verbose] = true end o.on("--debug", "Show debug messages and keep intermediate output") do |v| # Bio::Log::CLI.trace('debug') options[:debug] = true end o.separator "" o.on_tail('-h', '--help', 'display this help and exit') do options[:show_help] = true end end opts.parse!(ARGV) BIOVCF_VERSION=version BIOVCF_BANNER = "bio-vcf #{version} (biogem Ruby #{RUBY_VERSION} with pcows) by Pjotr Prins 2015-2020\n" $stderr.print BIOVCF_BANNER if !options[:quiet] if options[:show_help] print opts print USAGE exit 1 end if RUBY_VERSION =~ /^1/ $stderr.print "WARNING: bio-vcf runs on Ruby 2.x only\n" end $stderr.print "Options: ",options,"\n" if !options[:quiet] if options[:template] include BioVcf::RDF require 'bio-vcf/template' fn = options[:template] raise "No template #{fn}!" if not File.exist?(fn) # template = ERB.new(File.read(fn)) template = Bio::Template.new(fn) end stats = nil if options[:statistics] options[:num_threads] = nil stats = BioVcf::VcfStatistics.new end # Check for option combinations raise "Missing option --ifilter" if options[:ifilter_samples] and not options[:ifilter] raise "Missing option --efilter" if options[:efilter_samples] and not options[:efilter] raise "Missing option --sfilter" if options[:sfilter_samples] and not options[:sfilter] # raise "Soft filter not supported with --ifilter" if options[:add_filter] and options[:ifilter] # raise "Soft filter not supported with --efilter" if options[:add_filter] and options[:efilter] if options[:samples] samples = options[:samples].map { |s| s.to_i } end include BioVcf # Parse the header section of a VCF file (chomping STDIN) def parse_header line, samples, options header = VcfHeader.new(options[:debug]) header.add(line) print line if not options[:skip_header] STDIN.each_line do | headerline | if headerline !~ /^#/ # If no records in VCF, we never get here line = headerline break # end of header end header.add(headerline) if not options[:skip_header] if headerline =~ /^#CHR/ # The header before actual data contains the sample names, first inject the BioVcf meta information print header.tag(options),"\n" if options[:tag] and not options[:skip_header] # Then the additional filter(s) # ##FILTER= add_filter = options[:add_filter] if add_filter print "##FILTER=\n" end selected = header.column_names if samples newfields = selected[0..8] samples.each do |s| newfields << selected[s+9] end selected = newfields end print "#",selected.join("\t"),"\n" else print headerline end end end print header.printable_header_line(options[:set_header]),"\n" if options[:set_header] VcfRdf::header if options[:rdf] if line =~ /^#/ # We did not read a record line = nil end return header,line end # Parse a VCF line and return the (template) result as a string buffer def parse_line line,header,options,bedfilter,samples,template,stats=nil fields = VcfLine.parse(line) rec = VcfRecord.new(fields,header) r = rec # alias filter = options[:filter] sfilter = options[:sfilter] efilter = options[:efilter] ifilter = options[:ifilter] add_filter = options[:add_filter] # contains a filter name (soft filter) seval = options[:seval] ignore_missing = options[:ignore_missing] quiet = options[:quiet] set_filter_field = nil if sfilter or efilter or ifilter or seval # check for samples header_samples = header.column_names[9..-1] raise "Empty sample list, can not execute query!" if not header_samples end # -------------------------- # Filtering and set analysis if bedfilter bed = bedfilter.contains(rec) return if not bed end skip = lambda { |&m| matched = m.call if add_filter set_filter_field = true if matched false # always continue processing with an add-filter else not matched end } if filter return if skip.call { rec.gfilter(filter,ignore_missing_data: ignore_missing,quiet: quiet) } end if sfilter # sample 'or' filter rec.each_sample(options[:sfilter_samples]) do | sample | return if skip.call { sample.sfilter(sfilter,ignore_missing_data: ignore_missing,quiet: quiet) } end end if ifilter # include sample filter found = false rec.each_sample(options[:ifilter_samples]) do | sample | if sample.ifilter(ifilter,ignore_missing_data: ignore_missing,quiet: quiet) found = true break end end # Skip if there are no matches return if skip.call {found} end if efilter # exclude sample filter rec.each_sample(options[:efilter_samples]) do | sample | return if skip.call{ sample.efilter(efilter,ignore_missing_data: ignore_missing,quiet: quiet) } end end stats.add(rec) if stats # ----------------------------- # From here on decide on output rec.add_to_filter_field(add_filter) if set_filter_field if samples # Select certain samples for output newfields = fields[0..8] samples.each do |s| newfields << fields[s+9] end fields = newfields end if options[:eval] or seval begin results = nil # result string if options[:eval] res = rec.eval(options[:eval],ignore_missing_data: ignore_missing,quiet: quiet) results = res if res end if seval list = (results ? [] : [rec.chr,rec.pos]) rec.each_sample(options[:sfilter_samples]) { | sample | list << sample.eval(seval,ignore_missing_data: ignore_missing,quiet: quiet) } results = (results ? results.to_s + "\t" : "" ) + list.join("\t") end rescue => e $stderr.print "\nLine: ",line $stderr.print "ERROR evaluating --eval <#{options[:eval]}> #{e.message}\n" raise if options[:verbose] exit 1 end return results.to_s+"\n" if results else if options[:rdf] # Output Turtle RDF VcfRdf::record(options[:id],rec,options[:tags]) elsif options[:template] # Use ERB template begin template.body(binding) rescue Exception => e $stderr.print e,": ",fields,"\n" $stderr.print e.backtrace.inspect if options[:verbose] raise end elsif options[:rewrite] # Default behaviour prints VCF line, but rewrite info eval(options[:rewrite]) (fields[0..6]+[rec.info.to_s]+fields[8..-1]).join("\t")+"\n" elsif stats # do nothing else # Default behaviour prints VCF line fields.join("\t")+"\n" end end end CHUNK_SIZE = options[:thread_lines] pcows = PCOWS.new(options[:num_threads],CHUNK_SIZE,'bio-vcf',options[:timeout], options[:quiet],options[:debug]) header = nil header_output_completed = false chunk_lines = [] line_number=0 if options[:bed] bedfilter = BedFilter.new(options[:bed]) end begin # Define linear parser function (going through one chunk) process = lambda { | lines | res = [] lines.each do | line | res << parse_line(line,header,options,bedfilter,samples,template,stats) end res } # ---- Main loop STDIN.each_line do | line | line_number += 1 # ---- Skip embedded headers down the line... next if header_output_completed and line =~ /^#/ # ---- In the following section header information is handled - # this only happens once. # ---- Parse the header lines (chomps from STDIN) # and returns header info and the current line if line =~ /^#/ header, line = parse_header(line,samples,options) if line.nil? # No line after header, to there are no records to process break end end # p [line_number,line] # ---- After the header continue processing if not header_output_completed # one-time post-header processing if not options[:efilter_samples] and options[:ifilter_samples] # Create exclude set as a complement of include set options[:efilter_samples] = header.column_names[9..-1].fill{|i|i.to_s}-options[:ifilter_samples] end print template.header(binding) if template header_output_completed = true end if options[:eval_once] # this happens if we only want one line evaluated - say to get # the number of samples print parse_line(line,header,options,bedfilter,samples,template,stats) exit 0 end # ---- Lines are collected in one buffer and the lines buffer # is added to the chunks list (for the threads) chunk_lines << line # ---- In the following section the VCF lines are parsed by chunks # The chunks may go into different threads if chunk_lines.size >= CHUNK_SIZE # ---- process one chunk $stderr.print '.' if not options[:quiet] pcows.wait_for_worker_slot() pcows.submit_worker(process,chunk_lines) pcows.process_output() chunk_lines = [] end end pcows.submit_final_worker(process,chunk_lines) pcows.wait_for_workers() pcows.process_remaining_output() print template.footer(binding) if template stats.print if stats rescue Exception => e if e.message != 'exit' $stderr.print "ERROR: " $stderr.print e.message,"\n" end pcows.cleanup() raise if options[:verbose] exit 1 end bio-vcf-0.9.5/bio-vcf.gemspec000066400000000000000000000022461400124230400157360ustar00rootroot00000000000000# No longer generated by jeweler # -*- encoding: utf-8 -*- Gem::Specification.new do |s| s.name = "bio-vcf" s.version = File.read("VERSION") s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= s.authors = ["Pjotr Prins"] s.description = "Smart lazy multi-threaded parser for VCF format with useful filtering and output rewriting (JSON, RDF etc.)" s.email = "pjotr.public01@thebird.nl" s.executables = ["bio-vcf"] s.extra_rdoc_files = [ "LICENSE.txt", "README.md" ] s.files = [ ".travis.yml", "Gemfile", "LICENSE.txt", "README.md", "Rakefile", "VERSION", "bin/bio-vcf", "bio-vcf.gemspec", "ragel/gen_vcfheaderline_parser.rl", "ragel/generate.sh", ] s.files += Dir['lib/**/*.rb'] + Dir['bin/*'] s.files += Dir['[A-Z]*'] + Dir['test/**/*'] + Dir['features/**/*'] + Dir['template/**/*'] s.homepage = "http://github.com/vcflib/bio-vcf" s.licenses = ["MIT"] s.require_paths = ["lib"] s.required_ruby_version = Gem::Requirement.new(">= 2.0.0") # s.rubygems_version = "2.0.3" s.summary = "Fast multi-purpose multi-threaded VCF parser" end bio-vcf-0.9.5/doc/000077500000000000000000000000001400124230400136055ustar00rootroot00000000000000bio-vcf-0.9.5/doc/Compare_VCFs.md000066400000000000000000000071531400124230400164040ustar00rootroot00000000000000# Comparing VCF files Between two different pipeline runs we ended up with different VCF files. The starting point (BAMs) was the same, but in each pipeline different procedures may have been followed, i.e. the processing steps for variant calling were not exactly the same. The first freebayes+varscan2 pipeline (P1) I wrote after testing many callers including somatic sniper and strelka, so I should know that well enough. The second pipeline (P2) includes more variant callers. To find out how they compared and which output was preferred I decided to do some analysis using bio-vcf. ## Comparing freebayes output The freebayes somatic variant calling files differed in size. Just looking at one sample P1 had 479 lines and P2 had 729. The germline calls, however, where comparable in size. But when I ran a diff it showed these differed significantly too: wc -l germline*vcf 3527 germline1.vcf 3500 germline2.vcf cat germline1.vcf|bio-vcf -e "[r.chr,r.pos]"|sort > germline1.txt cat germline2.vcf|bio-vcf -e "[r.chr,r.pos]"|sort > germline2.txt diff germline1.txt germline2.txt |wc 1751 To zoom in on settings, lets look at read depth on chromosome 7 (-v and --num-threads=1 options I typically use when trying new filters because they give digestable output): cat germline1.vcf|bio-vcf -v --num-threads 1 --filter 'rec.chr=="7"' -e '[r.chr,r.pos,r.info.dp]'|sort 7 90225928 34 7 95216394 69 7 97821397 97 7 97821398 98 7 97822115 96 7 97822210 94 7 98503849 109 7 98543545 68 7 98543546 69 7 98582562 38 7 98650051 48 7 99690690 78 7 99690747 27 7 99693552 34 cat germline2.vcf|bio-vcf -v --num-threads 1 --filter 'rec.chr=="7"' -e '[r.chr,r.pos,r.info.dp]'|sort 7 90225928 121 7 95216394 534 7 97822115 1053 7 97822210 1044 7 97834704 249 7 98503849 1579 7 98547176 59 7 98553739 21 7 98648517 75 7 98650051 344 7 99690690 455 7 99690747 168 7 99693552 107 OK, this is informative. P1 called variants after removing duplicate reads. P2 did not. That explains the different in number of variants called. Unfortunately the sequencing concerns an FFPE dataset. FFPE degrades over time and DNA changes. In itself this is not a problem because we sequence many cells and the changed ones do not necessarily dominate. We do, however, amplify the DNA before sequencing through a PCR-type process. This means that randomly these FFPE changes may become dominant at a certain position and variant callers score them as genuine variants. I have studied this data and there is ample evidence of this effect. The only way to address this is by removing duplicate reads - so the amplified reads get compressed into one (theoretically, because sometimes there are multiple errors confusing things a bit). Removing duplicates is the *only* way and this can not happen *after* variant calling. This means P2 is out of the window. It is useless data also for the other variant callers. I don't even have to check the somatic calling. ## Conclusion A simple read depth check with bio-vcf proved that P2 had no merit. Either we rerun it after removing duplicates or we rely on P1. bio-vcf-0.9.5/doc/GATK_comparison.md000066400000000000000000000211701400124230400171100ustar00rootroot00000000000000# Comparing two large GATK files This is the exercise to explore the differences in the full BWA-GATK pipeline vs. a chunking-scatter-gather approach that is magnitudes faster. Using my tools [bio-vcf](https://github.com/pjotrp/bioruby-vcf), [bio-table](https://github.com/pjotrp/bioruby-table) and [bio-locus](https://github.com/pjotrp/bio-locus) interesting edge effects were found. The GATK output variant files are similar in size: -rw-r--r-- 1 pjotr users 992725762 Aug 29 11:22 HiSeqX_R1.fastq.sorted_dedup_realigned.bam.realigned.raw_variants.vcf -rw-r--r-- 1 pjotr users 987147441 Aug 29 11:26 HiSeqX_R1.fastq_dedup_realigned.bam.realigned.raw_variants.vcf Naming suggests the second one (scatter) is unsorted but it is actually sorted. Install bio-vcf, add it to the path if required, and you should see gem env export PATH=$GEM_HOME/bin:PATH gem install bio-vcf bio-vcf bio-vcf 0.9.0 (biogem Ruby 2.1.2 with pcows) by Pjotr Prins 2015 Create simple position files with calls /usr/bin/time -v bio-vcf -e '[r.chrom,r.pos,r.alt]' < scatter/HiSeqX_R1.fastq_dedup_realigned.bam.realigned.raw_variants.vcf > scatter_calls.vcf /usr/bin/time -v bio-vcf -e '[r.chrom,r.pos,r.alt]' < full/HiSeqX_R1.fastq.sorted_dedup_realigned.bam.realigned.raw_variants.vcf > full_calls.vcf Count the calls (we are ignoring the limited header info) wc -l scatter_calls.vcf 4773423 scatter_calls.vcf wc -l full_calls.vcf 4795998 full_calls.vcf (4795998-4773423)/4795998*100 or 0.5%. Do a diff and count de diffs egrep -c '^>' calls.diff 30401 egrep -c '^<' calls.diff 52976 52976/4795998*100 or 1.1% of different calls, hmmm. Remove the GL contig grep -v GL00 calls.diff > calls_wo_GL00.diff egrep -c '^<' calls_wo_GL00.diff 48797 Now install bio-table and bio-locus gem install bio-table bio-table bio-table 1.0.0 Copyright (C) 2012-2014 Pjotr Prins gem install bio-locus bio-locus bio-locus 0.0.6 (biogem Ruby 2.1.2) by Pjotr Prins 2014 Create a new VCF file using the diff information. Find all the calls egrep '^(<|>)' calls_wo_GL00.diff |grep -v GATKCommandLine| grep -v CHROM > all_diff.txt bio-table --columns 0,1 < all_diff.txt > chrom_pos_diff.txt with vi remove first > and < and make sure there is a tab: %s/^..//g %s/$/^INA/g Now use bio-locus to create full VCF files containing only these entries bio-locus --store --alt exclude < chrom_pos_diff.txt bio-locus 0.0.6 (biogem Ruby 2.1.2) by Pjotr Prins 2014 Stored 73644 positions out of 75414 in locus.db (1770 duplicate hits) bio-locus --match --alt exclude < ../full/HiSeqX_R1.fastq.sorted_dedup_realigned.bam.realigned.raw_variants.vcf > diff_full.vcf bio-locus --match --verbose -d < ../scatter/HiSeqX_R1.fastq_dedup_realigned.bam.realigned.raw_variants.vcf > diff_scatter.vcf (note: bio-locus is - still - a slow tool) Interestingly there is very little overlap between the call positions (only 1770 are shared)... wc -l diff*.vcf 48903 diff_full.vcf 26731 diff_scatter.vcf So, arguably the difference is (48903+26731)/4795998*100 or 1.6% of calls. Now we can compare the call contents bio-vcf -i -e '[r.chrom,r.pos,r.info.af]' --seval 's.dp' < diff_scatter.vcf > diff_scatter_af_sdp.txt For those that do match we see a difference in sample read depth pointing out the two methods differ in placing reads. So, let's see if we can find significant differences in frequency and read depth. First I am reducing the data to one chromosome to be able to work a bit faster bio-vcf --filter 'r.chrom=="3"' < ../full/HiSeqX_R1.fastq.sorted_dedup_realigned.bam.realigned.raw_variants.vcf > full.vcf bio-vcf --filter 'r.chrom=="3"' < ../scatter/HiSeqX_R1.fastq_dedup_realigned.bam.realigned.raw_variants.vcf > scatter.vcf wc -l *.vcf 301922 full.vcf 300326 scatter.vcf bio-vcf -i -e '[r.pos,r.alt,r.info.af]' --seval 's.dp' < full.vcf > full_af_dp.txt bio-vcf -i -e '[r.pos,r.alt, r.info.af]' --seval 's.dp' < scatter.vcf > scatter_af_dp.txt wc -l *.txt 40001 full_af_dp.txt 40001 scatter_af_dp.txt diff scatter_af_dp.txt full_af_dp.txt |grep -c '>' 2189 Differences typically look like < 402884 G 0.5 26 < 403020 A 0.5 21 --- > 402884 G 0.5 29 > 403020 A 0.5 25 i.e. the scatter approach has a different read depth 26 instead of 29 and 21 instead of 25 - reads end up in other places. Frequency-wise we don't see much differentce. More intriguing, a difference would be 1525d1529 < 663038 CATATGTTATATGTGTATGTATTGTATACAT 1.0 4 where an extra call for an insertion was made in the scatter approach with a DP of 4. Now let's quantify how much DP differs Combine the tables bio-table --columns 0,3 < full_af_dp.txt > f_dp.txt bio-table --columns 0,3 < scatter_af_dp.txt > s_dp.txt bio-table --merge f_dp.txt s_dp.txt > merged.txt After editing the table header to show 'pos\tfull\tscatter' bio-table --num-filter 'value[1]!=value[0]' < merged.txt |wc -l 2416 it shows that for chromosome 3, 2416 calls out of 301922 (0.8%) have a different read depth. bio-table --verbose --debug --num-filter '(value[1]-value[0]).abs > 3' < merged_no_NA.txt|wc -l 356 356 (0.1% of total calls) showed a read depth difference larger than 4 reads. And 61 showed a read depth difference larger than 10 reads: fedor13:~/bcosc/gvcf/chr3$ bio-table --verbose --debug --num-filter '(value[1]-value[0]).abs > 10' < merged_no_NA.txt bio-table 1.0.0 Copyright (C) 2012-2014 Pjotr Prins INFO bio-table: Array: [{:show_help=>false, :write_header=>true, :skip=>0, :debug=>true, :num_filter=>"(value[1]-value[0]).abs > 10"}] DEBUG bio-table: Filtering on (value[1]-value[0]).abs > 10 INFO bio-table: Array: ["pos", "full", "scatter"] pos full scatter 855606 24 9 855609 24 10 855610 24 10 855617 22 9 1432738 17 3 1434184 35 22 3173353 37 7 3713421 42 11 3713601 31 13 3713646 39 24 3713647 39 24 3713669 43 29 3714214 33 19 3762444 18 3 3764753 29 15 3764808 29 15 3764830 26 15 3764904 22 11 3764918 24 13 3937379 26 13 3937468 19 7 4005161 17 4 4005568 35 22 4297382 27 13 4297644 34 20 4958959 31 10 4958960 31 10 4959272 35 11 4959609 27 9 4960175 27 5 6159995 17 0.5 8432601 34 23 8432973 24 13 8432986 26 15 11414301 12 28 11414307 12 28 11414313 12 28 11414323 12 28 11528593 21 6 12070044 39 23 12070272 34 18 12071772 34 22 15010075 27 16 17740441 43 27 17740468 52 33 18367833 26 13 18367863 29 16 18367950 32 19 18973094 39 27 18976962 30 16 18977299 20 8 19000198 42 29 19000214 40 26 19898931 15 2 19898945 13 2 19898997 16 5 19899206 37 24 21293536 40 25 21293836 26 15 21294685 36 24 Based on this information (you can see clustering at certain 'hot spots') I suspect that these are border effects in the regions where chunking took place. Note also that scatter more often has *less* reads which means we are missing reads because of edges (it is a BWA thing). Even so, even *with* these downsides, the method may work for rapid diagnostics, provided the chunking affected FN/FP calls do not fall in the regions of interest. For this setup, where time to diagnostic counts (including cancer), it may prove a valuable approach. I also suggest we find a way of setting chunking in regions of little interest (outside coding genes and or regions of low variation as Brad suggested). bio-vcf-0.9.5/doc/GTEx_reduce.md000066400000000000000000000657671400124230400163120ustar00rootroot00000000000000# Reduce number of GTEx SNPs This exercise aims to reduce the number of SNPs in a GTEx VCF file for the purpose of eQTL mapping. The original VCF is about 88 GB and contains 11.5 million SNPs (included imputed SNPs) We look at applying the following rules 1. Check for number of samples 2. If no call > 5% then delete 3. If the imputation r2 value is less than 0.3 throw the imputed SNP away 4. If the MAF is < 5% delete 5. If the r2 of LD is >.90 we can perhaps delete as redundant The original VCF file is huge, so after (interrupted) unpacking reduce it to ~250K lines for the purpose of fast testing turnaround: head -250000 /mnt/big/user/pjotr/gtex.vcf > gtex.vcf time wc gtex.vcf 250000 114742296 1945309272 gtex.vcf real 0m24.592s user 0m24.197s sys 0m0.396s which allows reading a 2GB file in half a minute. Also created a 1000 line file to have even faster turnaround named GTEx-tiny.vcf. ## Install bio-vcf There are multiple ways to install bio-vcf. The preferred route is to use GNU GUix. Basically, after installing guix, install guix package -i ruby-bio-vcf If that is not available (work in progress) install Ruby, set the environment and install the bio-vcf gem. gem install bio-vcf This should show bio-vcf -h ## Install pigz For fast gz unpacking guix package -i pigz ## Check for number of genotypes (samples) For locating QTL GTEx uses at least 70 samples per tissue to have enough statistical power to map eQTL (out of 450 individuals). That is RNA-seq data, not genotype data. When a sample has a genotype the GT field is set, otherwise it looks like './.' (i.e.. best Guessed Genotype with posterior probability threshold of 0.9). E.g. with cat orig/GTEx-tiny.vcf ./bin/bio-vcf --eval '[r.chr,r.pos]' --seval 's.gt' 1 900002 0/1 1/1 0/0 ./. ./. 0/0 ./. ./. ./. ./. 0/1 ./. ./. 0/0 ./. ./. ./. ./. 0/1 0/1 ./. ./. ./. ./. ./. 0/0 1/1 0/1 ./. ./. 0/1 ./. ./. ./. ./. ./. 0/1 the matching posterior probability of the genotype looks like ./bin/bio-vcf --eval '[r.chr,r.pos]' --seval 's.gl.join(",")' 1 899987 0.995,0.005,0 1.0,0,0 1.0,0,0 0.918,0.082,0 0.995,0.005,0 0.991,0.009,0 0.918,0.082,0 0.993,0.007,0 0.979,0.021,0 0.997,0.003,0 1.0,0,0 0.96,0.04,0 0.884,0.116,0 0.994,0.006,0 0.992,0.008,0 0.956,0.044,0 0.949,0.051,0 0.998,0.002,0 0.963,0.037,0 0.443,0.457,0.1 0.931,0.069,0 0.938,0.062,0 0.91,0.09,0 0.336,0.662,0.002 0.939,0.061,0 0.998,0.002,0 0.994,0.006,0 0.998,0.002,0 1.0,0,0 0.899,0.101,0 0.005,0.995,0 1.0,0,0 0.953,0.047,0 1.0,0,0 0.915,0.085,0 so calls are in there which have a low posterior probability. We can also filter on samples called (which are not "./.") now with ./bin/bio-vcf --filter 'r.samples.count {|s| s.gt!="./."}>100' < orig/GTEx-tiny.vcf which has minor impact, but does remove some. ## If no call > 5% then delete Lets check for genotypes called. This rule is more stringent ./bin/bio-vcf --eval '[(r.samples.count{|s| s.gt!="./."}>427)]' stripped out about 50% of the calls (427 is 95\%). ## If the imputation r2 value is less than 0.3 throw the imputed SNP away The number of imputed SNPS is around 90%. Assuming this value is captured in info.impinfo ("Measure of the observed statistical in formation associated with the allele frequency estimate") we can do ./bin/bio-vcf --eval '[r.info.type == 0 && r.info.impinfo > 0.3]' < orig/GTEx-tiny.vcf removes about 7% of calls (type 0 is imputed, actually we can skip this check because impinfo is 1.0 for non-imputed). Increasing IMPINFO to 0.5 removes 10% of SNPs and 0.7 removes almost 40% of SNPs. ## If the MAF is < 5% delete Calculating the minor allele frequency (MAF) is possible. 5% is a good choice for a dataset this size unless we are looking for rare SNPs (and we should keep all). Using the filter would suggest ./bin/bio-vcf --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1]< orig/GTEx-tiny.vcf 1 894573 PASS 0.809 1 894719 maf05 0.015 1 895037 maf05 0.022 1 895268 maf05 0.037 1 899000 maf05 0.024 1 899928 PASS 0.867 1 899937 PASS 0.826 1 899938 PASS 0.831 1 899942 PASS 0.835 that the MAF is actually the minor allele frequency here for smaller values of EXP freq. This means we can filter on EXP ./bin/bio-vcf --filter 'r.info.exp_freq_a1 > 0.05' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1,r.info.type,r.info.impinfo] < orig/GTEx-tiny.vcf which removes ~50% of calls. I caught SNPs that actually have an AF<0.05, e.g. 1 759970 PASS 0.049 0 0.975 Maybe round-off error or a result of imputation. ## If the r2 of LD is >.90 we can perhaps delete as redundant The VCF file contains an info field named HW or the "Hardy Weinberg Equilibrium P value". The Hardy - Weinberg Equilibrium p<1x10-6 has been calculated using the software tool SNPTEST. Filtering on HW: ./bin/bio-vcf --filter 'r.info.hw < 0.9' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1,r.info.type,r.info.impinfo,r.info.hw] < orig/GTEx-tiny.vcf|wc reduces the set by about 60%. Filtering on 0.95 or 0.85 has little effect. Simply filtering on <1.0 amounts to practically the same. ## Combining above rules ./bin/bio-vcf --filter 'r.info.exp_freq_a1 > 0.05 and r.info.exp_freq_a1 < 0.95 and r.info.impinfo > 0.3 and r.info.hw < 1.0 and (r.samples.count{|s| s.gt!="./."}>427)' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1,r.info.type,r.info.impinfo,r.info.hw] < orig/GTEx-tiny.vcf Throws out ~83% of calls. Note, as discussed below, we are also throwing out all SNPs with AF>0.95. To get some sense of contributions: Removing 'r.info.exp_freq_a1 > 0.05' throws out 55% of calls instead. Removing 'r.info.exp_freq_a1 < 0.95' throws out 62% of calls instead. Removing 'r.info.impinfo > 0.3' makes no difference. Removing 'r.info.hw < 1.0' throws out 79% of calls instead. Removing '(r.samples.count{|s| s.gt!="./."}>427)' throws out 62% of calls instead. In other words IMPINFO appears to be covered by the others and AF>0.95 is (largely) covered by the sample count. ## On imputed SNPs Missing DNA data is pretty nasty when it comes to calculating SNPs (or SNVs). Missing data is a result of missing or misaligned sequence reads. Some samples (read individuals) do better than others, partly due to noise (technical), distance from the reference genome (biology) and structural variation in the genome (undiscovered INDELS). When one has sequenced a population it is possible to impute missing data to some degree. This is done through LD. Here is a pretty good explanation how imputation is done: http://steventsnyder.com/projects/imputation/imputationtalk.pdf For GTEx they used IMPUTE2 http://www.nature.com/ng/journal/v44/n8/full/ng.2354.html which does something pretty similar using 1000 genome Phase 3 (actually I would think the correct way to do this is to tie in structural variation analysis and revisit the reads for every sample, but that is a separate story/exercise). An imputed SNP is actually a real SNP in some samples and a calculated SNP in others. IMPUTE2 attaches a 'probability' for the imputation. Say we have 20 real SNPs and 20 imputed SNPs, you'd expect the probability to be 0.5. 40 real SNPs out of 40 would be 1.0 (it is probably a bit more involved than that because sample size matters and of course LD, but it should generally be like this). Simply throwing away 20 real SNPs in the first case by default does not look right. What I am proposing is to retain imputed SNPs based on their number (higher is good) and the probability (higher is good). A number larger than 20% and a probability higher than 0.8 could make sense. At the same time, a high probability will reflect a high LD. So, for the purpose of GWAS we could actually select the range 0.5 0.05 and r.info.exp_freq_a1 < 0.95 and r.info.impinfo > 0.3 and r.info.hw < 1.0 ' --eval '[r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1,r.info.type,r.info.impinfo,r.info.hw,r.info.miss]' < orig/GTEx-tiny.vcf which is quite a bit faster. Column 4 (AF) and column 5 (IMPINFO) are the `informative' columns. The 4th row shows an AF of 4.4% with IMPINFO 0.982, same for the 3rd row. Meanwhile the 2nd row shows low AF scored in most of the samples(!) and the imputation info is 0.742. What does it mean? Let's get some detail ./bin/bio-vcf --num-threads 1 --eval '[r.chr,r.pos,r.info.type,r.info.EXP_FREQ_A1,r.info.impinfo,r.info.miss,(r.samples.count{|s| s.gt!="./."})]' --seval '[s.gt,s.gl[0]]' < GTEx-tiny.vcf 1 897879 0 0.012 0.742 0.02 441 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 ./. 0.45 0/0 1.0 0/0 1.0 0/0 1.0 0/0 0.917 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 0.997 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/1 0.001 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 ./. 0.191 0/0 0.999 ./. 0.718 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 0.996 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/1 0.087 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 1.0 0/0 0.995 0/0 0.999 0/0 1.0 0/0 It turns out the GL which is the posterior probability that a sample matches a genotype defines whether a sample has been scored. You can see that one sample was scored as genotype 0/1 with a posterior of 0.087 for the SNP genotype 0/0. Ther are also samples that have a posterior <1.0, but they are few in this case. When we look at 90002 we can see a more mixed up result: 1 900002 0 0.61 0.593 0.7222 125 0/1 0.01 1/1 0 0/0 1.0 ./. 0 ./. 0.284 0/0 0.997 ./. 0.013 ./. 0.001 ./. 0.001 ./. 0.002 0/1 0.052 ./. 0.01 ./. 0.249 0/0 0.974 ./. 0.027 ./. 0.023 ./. 0.018 ./. 0.272 0/1 0.092 0/1 0.004 ./. 0.026 ./. 0.031 ./. 0.035 ./. 0.108 ./. 0.116 0/0 0.911 1/1 0 0/1 hardly the level of confidence we are looking for (IMPINFO is 0.6). Finally when looking at 1 899942 0 0.835 0.722 0.3311 301 ./. 0.753 ./. 0.751 0/1 0 1/1 0.937 1/1 0.999 0/0 0 ./. 0.891 ./. 0.858 ./. 0.492 1/1 0.908 1/1 1 1/1 0.919 1/1 0.998 0/1 0.001 1/1 0.983 1/1 0.933 1/1 0.934 1/1 0.998 0/1 0 ./. 0 1/1 0.939 1/1 0.938 1/1 0.906 ./. 0 1/1 0.991 1/1 1 ./. 0.877 1/1 897879 and 899942 have similar IMPINFO (0.7) For 897879 the number of '0/0' was 436 out of 441. The ones that had a GL of 1.0 was 411. One score for imputation could be the number of samples imputed, which would be 1-411/441 = 7% And with ./bin/bio-vcf --num-threads 1 --eval '[r.chr,r.pos,r.info.type,r.info.EXP_FREQ_A1,r.info.impinfo,r.info.miss,(r.samples.count{|s| s.gt=="1/1" and s.gl[2]==1.0})]' < orig/GTEx-tiny.vcf For 899942 the number of '1/1' was 238 out of 301. The ones that had a GL of 1.0 was 76. The number of samples imputed would be 1-76/301 is 75%. The IMPINFO shows no relationship with the number of samples imputed. At least not in a way I would expect it. Looking online this document http://static-content.springer.com/esm/art%3A10.1007%2Fs00125-014-3256-2/MediaObjects/125_2014_3256_MOESM3_ESM.pdf suggests that the IMPINFO is r2. More on that below. Meanwhile filtering on the number of genotypes scored with high confidence using the GL could be interesting as a quality metric. There is another parameter named certainty "Average certainty of best-guess genotypes". Let's try filtering on that. ./bin/bio-vcf --num-threads 1 --eval '[r.chr,r.pos,r.info.type,r.info.EXP_FREQ_A1,r.info.impinfo,r.info.certainty,(r.samples.count{|s| s.gt=="1/1" and s.gl[2]==1.0})]' --filter 'r.info.certainty>0.9' < orig/GTEx-tiny.vcf removes 10% of SNPs. Trying it with the full filter, however, makes no difference. We'll try one more filter where we count the number of real SNPs first. ./bin/bio-vcf --eval '[r.chr,r.pos,r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) },r.samples.count{|s| s.gtindex!=nil}]' < orig/GTEx-tiny.vcf 1 898467 441 447 1 899000 390 434 1 899928 177 382 1 899937 90 292 1 899938 100 301 1 899942 103 301 1 899949 405 425 1 899987 89 312 1 899989 164 357 1 900002 18 125 1 900057 187 373 1 900169 421 439 shows the high confidence SNPs and the number of SNPs called. Now we play a bit with the settings. This being Ruby introduce some variables ./bin/bio-vcf --eval 'found=r.samples.count{|s| s.gt!="./."} ; real=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) } ; [r.chr,r.pos,real,found]' < orig/GTEx-tiny.vcf Let's say we do not allow less than 70% real, i.e. real/found>0.7 ./bin/bio-vcf --eval '[r.chr,r.pos,r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) },r.samples.count{|s| s.gt!="./."}]' --filter 'r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f/r.samples.count{|s| s.gt!="./."}>0.7' < orig/GTEx-tiny.vcf reduces the set by 35%. Also we don't want more than 30 actual imputed values. That means ./bin/bio-vcf --eval '[r.chr,r.pos,r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) },r.samples.count{|s| s.gt!="./."}]' --filter 'found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; total-found<30' < orig/GTEx-tiny.vcf reduces the set by 60%. Increasing that value to 50 makes it 50%. Filling it in the original filter we are now down to 13%: ./bin/bio-vcf --filter 'found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; r.info.miss < 0.05 and found/total>0.7 and total-found<30 and r.info.exp_freq_a1 > 0.05 and r.info.exp_freq_a1 < 0.95 and r.info.impinfo > 0.7 and r.info.hw < 1.0' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1,r.info.type,r.info.impinfo,r.info.hw] < orig/GTEx-tiny.vcf and speeding it up a bit with lambda: ./bin/bio-vcf --filter '((r.info.miss<0.05 and r.info.exp_freq_a1>0.05 and r.info.exp_freq_a1<0.95 and r.info.impinfo>0.7 and r.info.hw<1.0) ? (lambda { found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; found/total>0.7 and total-found<30 }.call) : false)' < orig/GTEx-tiny.vcf ### Further digging on IMPINFO GTEx Science paper suggests https://www.sciencemag.org/content/suppl/2015/05/06/348.6235.648.DC1/GTEx.SM.pdf (IMP)INFO is the imputation quality score coming out of IMPUTE2. According to their manual INFO is a measure of the observed statistical information associated with the allele frequency estimate (hopefully before imputation). See also https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#info_metric_details This metric is similar to the r2 reported by other programs like MaCH and Beagle. Although each of these metrics is defined differently, they tend to be correlated. Our metric typically takes values between 0 and 1, where values near 1 indicate that a SNP has been imputed with high certainty. The metric can occasionally take negative values when the imputation is very uncertain, and we automatically assign a value of -1 when the metric is undefined (e.g., because it wasn't calculated). Investigators often use the info metric to remove poorly imputed SNPs from their association testing results. There is no universal cutoff value for post-imputation SNP filtering; various groups have used cutoffs of 0.3 and 0.5, for example, but the right threshold for your analysis may differ. One way to assess different info thresholds is to see whether they produce sensible Q-Q plots, although we emphasize that Q-Q plots can look bad for many reasons besides your post-imputation filtering scheme. This Sciencemag GTEx.SM.pdf document says: For eQTL analysis, following imputation, we filtered out the following SNPs: missing rate cutoff <95% for best - guessed genotypes at posterior probability>0.9, Hardy - Weinberg Equilibrium p<1x10-6 (using the software tool SNPTEST, imputation confidence score, INFO<0.4, and minor allele frequency, MAF<5%. This yielded 6,820,471 genotyped and imputed autosomal SNPs. I should be able to replicate this filter (all this data is in the VCF file). 7 million SNPs is still a lot for our purposes. When looking at my analysis I think we should increase IMPINFO to 0.7. The threshold at 0.5 shows a lot of variability. ## On common SNPs (or rare variants) Common SNPs are SNPs that occur in a large part of the population. Often these SNPs simply reflect a variant not seen in the reference genome (otherwise they would not even be scored!) and can therefore be considered harmless (no effect). In general practice these SNPs are thrown out of studies that look into biomedical effects. For GWAS, however, a common SNP wich correlates perfectly with some phenotype *is* of interest. If 95% of SNPs correlates with some gene expression it *could* be involved in regulation, for example. Throwing such a SNP out is throwing out the baby with the bath water. Interestingly in GTEx 75% of SNPs are common SNPs (450 genotyped individuals, threshold 90%). It would be really nice to throw these out from a data handling and computational angle, but I suspect it is not a great idea. Common SNPs are those that are scored in >95% of the population. This does mean that the other variants are rare. min(p,1-p) would be a good approximation - p can contain one variant or more, depending. Removing rare SNPs (now defined) is an interesting one. Do we throw the baby out with the bathwater? That is a valid question. Also, since we don't score reference alleles, we may miss out on a number of those too. Still, with rare diseases, for example, in a population of 450 you'd be lucky to find one SNP. And one single SNP certainly won't hold for significance. I think we'd be OK to set the threshold to 5% (and 95%) for the purpose of eQTL mapping. ## Final filtering Using pigz to unpack the gzip file we can see how fast bio-vcf is (effectively bio-vcf uses 10 cores here) pigz -c -d /mnt/big/GTEXv6_20151023/GTEx_Analysis_20150112_OMNI_2.5M_5M_450Indiv_chr1to22_genot_imput_info04_maf01_HWEp1E6_ConstrVarIDs.vcf.gz |/usr/bin/time -v | ./bin/bio-vcf --thread-lines 40000 --filter 'r.info.miss < 0.05 and r.info.exp_freq_a1 > 0.05 and r.info.exp_freq_a1 < 0.95 r.info.certainty>0.9 and r.info.impinfo > 0.7 and r.info.hw < 1.0' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1,r.info.type,r.info.impinfo,r.info.hw,r.info.miss] User time (seconds): 4004.84 System time (seconds): 209.98 Percent of CPU this job got: 980% Elapsed (wall clock) time (h:mm:ss or m:ss): 7:09.99 and speedwise bio-vcf compares favourably even to a bare pigz+wc /usr/bin/time -v pigz -c -d /mnt/big/GTEXv6_20151023/GTEx_Analysis_20150112_OMNI_2.5M_5M_450Indiv_chr1to22_genot_imput_info04_maf01_HWEp1E6_ConstrVarIDs.vcf.gz|wc User time (seconds): 346.61 System time (seconds): 183.30 Percent of CPU this job got: 44% Elapsed (wall clock) time (h:mm:ss or m:ss): 19:48.18 (wc is maxing out at 100% CPU). The original VCF contains 11.5 million SNPs (88 GB uncompressed VCF) and our filter rendered 4676425 SNPs. The number of SNPs we have now is about 4.5 million (40% of the total). Adding the imputation filter (so not allowing a large percentage of SNPs being calculated) reduces the file with pigz -c -d /mnt/big/GTEXv6_20151023/GTEx_Analysis_20150112_OMNI_2.5M_5M_450Indiv_chr1to22_genot_imput_info04_maf01_HWEp1E6_ConstrVarIDs.vcf.gz |/usr/bin/time -v ./bin/bio-vcf --filter 'found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; r.info.miss < 0.05 and found/total>0.7 and total-found<30 and r.info.exp_freq_a1 > 0.05 and r.info.exp_freq_a1 < 0.95 and r.info.impinfo > 0.7 and r.info.hw < 1.0' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1,r.info.type,r.info.impinfo,r.info.hw] > test2.vcf This command maxed out on 32-cores. It does a greedy count, so I reduced the number of thread-lines and rearranged the order a bit by postponing sample counts: pigz -c -d /mnt/big/GTEXv6_20151023/GTEx_Analysis_20150112_OMNI_2.5M_5M_450Indiv_chr1to22_genot_imput_info04_maf01_HWEp1E6_ConstrVarIDs.vcf.gz |/usr/bin/time -v ./bin/bio-vcf --thread-lines 10000 --filter '((r.info.miss<0.05 and r.info.exp_freq_a1>0.05 and r.info.exp_freq_a1<0.95 and r.info.impinfo>0.7 and r.info.hw<1.0) ? (lambda { found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; found/total>0.7 and total-found<30 }.call) : false)' User time (seconds): 125002.18 System time (seconds): 1324.05 Percent of CPU this job got: 2913% Elapsed (wall clock) time (h:mm:ss or m:ss): 1:12:16 that worked with a whopping 29 core usage taking 1hr and 12 min resulting in 3.9 million SNPS. This throws away imputed SNPs which may still be of interest. In the following we test AF for real calls and throw away imputed SNPs that have more than 30% calculated: pigz -c -d /mnt/big/GTEXv6_20151023/GTEx_Analysis_20150112_OMNI_2.5M_5M_450Indiv_chr1to22_genot_imput_info04_maf01_HWEp1E6_ConstrVarIDs.vcf.gz |/usr/bin/time -v ./bin/bio-vcf --thread-lines 10000 --filter '((r.info.miss<0.05 and r.info.exp_freq_a1>0.05 and r.info.exp_freq_a1<0.95 and r.info.impinfo>0.7 and r.info.hw<1.0) ? (lambda { found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; af=found/450 ; af>0.05 and af < 0.95 and found/total>0.3 }.call) : false)' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1] User time (seconds): 124262.48 System time (seconds): 1236.51 Percent of CPU this job got: 2879% Elapsed (wall clock) time (h:mm:ss or m:ss): 1:12:38 Now the number of SNPs have dropped to 1.2 million(!). This is very interesting. So, if we calculate the AF using truly called genotypes it drops significantly (even allowing 70% of genotypes to be imputed). Now, to make sure we don't remove fully called SNPs we need to add one more test for r.info.type>0 just to ascertain no SNPs marked as fixed get thrown away (should be slightly faster too) pigz -c -d /mnt/big/GTEXv6_20151023/GTEx_Analysis_20150112_OMNI_2.5M_5M_450Indiv_chr1to22_genot_imput_info04_maf01_HWEp1E6_ConstrVarIDs.vcf.gz |/usr/bin/time -v ./bin/bio-vcf --timeout 600 --thread-lines 10_000 --filter '((r.info.miss<0.05 and r.info.exp_freq_a1>0.05 and r.info.exp_freq_a1<0.95 and r.info.impinfo>0.7 and r.info.hw<1.0) ? ((r.info.type>0 and r.info.exp_freq_a1>0.05 and r.info.exp_freq_a1<0.95) or lambda { found=r.samples.count { |s| (!s.empty? && s.gl[s.gtindex]==1.0) }.to_f; total=r.samples.count{|s| s.gt!="./."} ; af=found/450 ; af>0.05 and af < 0.95 and found/total>0.3 }.call) : false)' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1] > t4a.txt User time (seconds): 100417.43 System time (seconds): 1114.03 Percent of CPU this job got: 2492% Elapsed (wall clock) time (h:mm:ss or m:ss): 1:07:53 This is an impressive one-liner which, unlike Perl-style one-liners, is still readable and does a lot of work normally captured in one-off scripts. In the final version we only allow 30% of calls to be imputed. pigz -c -d /mnt/big/GTEXv6_20151023/GTEx_Analysis_20150112_OMNI_2.5M_5M_450Indiv_chr1to22_genot_imput_info04_maf01_HWEp1E6_ConstrVarIDs.vcf.gz |/usr/bin/time -v ./bin/bio-vcf --timeout 900 --thread-lines 10_000 --filter 'snp_in_range = (r.info.miss<0.05 and r.info.exp_freq_a1>0.05 and r.info.exp_freq_a1<0.95 and r.info.impinfo>0.7 and r.info.hw<1.0) ; (snp_in_range ? ((r.info.type>0 and snp_in_range) or lambda { found=r.samples.count { |s| !s.empty? && s.gl[s.gtindex]==1.0 }.to_f; total=r.samples.count{|s| s.gt!="./."} ; af=found/450 ; af>0.05 and af < 0.95 and found/total>0.7 }.call) : false)' --eval [r.chr,r.pos,r.filter,r.info.EXP_FREQ_A1] -v > t4d.txt which is now down to 2 million SNPs. That is 1/5th of the original number and 1/3rd of the SNPs used for eQTL analysis in GTEx. Basically it says: filter out all SNPs that have an AF<5% or larger than 95%. We also filter out more than 5% missing genotypes, IMPINFO<0.7 and p(Harvey-Weinberg)=1.0. For imputed SNPs we filter out AF<5% on high-confidence genotypes and we only allow up to 30% of genotypes to be imputed within a SNP call. Most of the gain came from the last filter! bio-vcf-0.9.5/doc/Using_Mongo.md000066400000000000000000000254071400124230400163630ustar00rootroot00000000000000# Using bio-vcf with MongoDB bio-vcf can output many types of formats. In this exercise we will load Mongo with VCF data and do some queries on that. ## Install Mongo (Debian) With su (password 'bioinformatics') ```sh su apt-get install mongodb ``` ## Install Mongo in $HOME Mongo comes with many distributions. Here we installed with guix. Check ```sh guix package -A mongodb mongodb 3.3.3 out gn/packages/mongodb.scm:31:2 ``` Create a directory for the database ```sh mkdir -p ~/opt/var/mongodb mkdir -p ~/opt/etc ``` And create a configuration file ~/opt/etc/mongo.conf ``` verbose = true port = 27017 dbpath = /home/user/opt/var/mongodb/ noauth = true maxConns = 5 rest = true ``` and run Mongo ```sh env LC_ALL=C mongod --config ~/opt/etc/mongo.conf ``` ```ruby use admin db.createUser({user:"admin", pwd:"admin123", roles:[{role:"root", db:"admin"}]}) ``` ## Use client ```python mongo use admin db.createUser({user:"admin", pwd:"admin123", roles:[{role:"root", db:"admin"}]}) ``` or on a different host ```python mongo --host 192.168.1.24 ``` ## Tutorial Mongo Using the example on MongoDB's [website](https://docs.mongodb.org/getting-started/shell/import-data/) ### Load data Records look like: ```javascript {"address": {"building": "2780", "coord": [-73.98241999999999, 40.579505], "street": "Stillwell Avenue", "zipcode": "11224"}, "borough": "Brooklyn", "cuisine": "American ", "grades": [{"date": {"$date": 1402358400000}, "grade": "A", "score": 5}, {"date": {"$date": 1370390400000}, "grade": "A", "score": 7}, {"date": {"$date": 1334275200000}, "grade": "A", "score": 12}, {"date": {"$date": 1318377600000}, "grade": "A", "score": 12}], "name": "Riviera Caterer", "restaurant_id": "40356018"} {"address": {"building": "351", "coord": [-73.98513559999999, 40.7676919], "street": "West 57 Street", "zipcode": "10019"}, "borough": "Manhattan", "cuisine": "Irish", "grades": [{"date": {"$date": 1409961600000}, "grade": "A", "score": 2}, {"date": {"$date": 1374451200000}, "grade": "A", "score": 11}, {"date": {"$date": 1343692800000}, "grade": "A", "score": 12}, {"date": {"$date": 1325116800000}, "grade": "A", "score": 12}], "name": "Dj Reynolds Pub And Restaurant", "restaurant_id": "30191841"} ``` Note there are no specific identifiers. Or are there? ```sh wget https://raw.githubusercontent.com/mongodb/docs-assets/primer-dataset/primer-dataset.json mongoimport --db test --collection restaurants --drop --file primer-dataset.json Mon Apr 11 00:24:50.963 dropping: test.restaurants Mon Apr 11 00:24:52.375 check 9 25359 Mon Apr 11 00:24:52.448 imported 25359 objects ``` ### Use the shell Run the mongo shell with ```sh mongo ``` ```ruby use test db.restaurants.find() db.restaurants.find( { "borough": "Manhattan" } ) db.restaurants.find( { "grades.score": { $gt: 30 } } ) ... AND ... db.restaurants.find( { "cuisine": "Italian", "address.zipcode": "10075" ,"grades.score": { $gt: 30 }} ) ... OR ... db.restaurants.find( { $or: [ { "cuisine": "Italian" }, { "address.zipcode": "10075" } ] } ) ... SORT ... db.restaurants.find().sort( { "borough": 1, "address.zipcode": 1 } ) ... Count ... db.restaurants.aggregate( [ { $group: { "_id": "$borough", "count": { $sum: 1 } } } ] ); db.restaurants.aggregate( [ { $match: { "borough": "Queens", "cuisine": "Brazilian" } }, { $group: { "_id": "$address.zipcode" , "count": { $sum: 1 } } } ] ); ... Index ... db.restaurants.createIndex( { "cuisine": 1, "address.zipcode": -1 } ) ``` ### Prepare template with bio-vcf ```sh wget https://github.com/pjotrp/bioruby-vcf/raw/master/test/data/input/gatk_exome.vcf cat gatk_exome.vcf |bio-vcf --eval '[r.chr,r.pos]' ``` Let's create a template named gatk_template.json ```ruby { "rec": { "chr": "<%= rec.chrom %>", "pos": <%= rec.pos %>, "ref": "<%= rec.ref %>", "alt": "<%= rec.alt[0] %>", "dp": <%= rec.info.dp %> } } ``` And run it ```sh cat gatk_exome.vcf |bio-vcf --template gatk_template.json |less cat gatk_exome.vcf |bio-vcf --template gatk_template.json > gatk_exome.json ``` Looks like ``` { "rec": { "chr": "X", "pos": 134713855, "ref": "G", "alt": "A", "dp": 4 } } ``` Import into mongo mongo v. 2.0.6 ```sh mongoimport --db gatk --collection vcf --drop --file gatk_exome.json --jsonArray ``` mongo v. 3.2.3 ```sh mongoimport --db gatk --collection vcf --drop --file gatk_exome.json ``` ```ruby use gatk db.vcf.find() db.vcf.find( { "rec.chr": "X" } ) db.vcf.find( { "rec.chr": "X" } ).count() 3 db.vcf.find( { "rec.dp": { $gt: 5 }} ) db.vcf.find( { "rec.dp": { $gt: 5 }} ).count() 25 ``` Comparable bio-vcf statements ``` cat gatk_exome.vcf |bio-vcf --eval '[r.chr,r.pos,r.ref,r.alt,r.info.dp]' --filter "r.chr=='X'"|grep -v '#' |wc -l =>"[r.chr,r.pos,r.ref,r.alt,r.info.dp]", :filter=>"r.chr=='X'"} 3 cat gatk_exome.vcf |bio-vcf --eval '[r.chr,r.pos,r.ref,r.alt,r.info.dp]' --filter "r.info.dp>5"|grep -v '#' |wc -l =>"[r.chr,r.pos,r.ref,r.alt,r.info.dp]", :filter=>"r.info.dp>5"} 25 ``` Exercise 1. With bio-vcf take the field "Variant Confidence/Quality by Depth" and filter on QD>12.0. How many matches? Answer 112 out of 175 Exercise 2. Do the same with MongoDB. So you can do ```ruby db.vcf.find( { "rec.qd": { $gt: 12.0 }} ).count() 112 ``` ## Now for some real data Let's use our PIK3CA data in two samples ``` cat gene_PIK3CA.vcf |bio-vcf --samples 2,3 --seval s.dp cat gene_PIK3CA.vcf |bio-vcf --sfilter-samples 2,3 --seval s.dp --sfilter "s.dp>7" cat gene_PIK3CA.vcf |bio-vcf --sfilter-samples 0,3 --sfilter 's.dp>20' --seval s.dp 3 178916645 24 39 3 178916651 30 31 3 178921407 32 43 3 178936082 24 24 3 178936091 27 32 3 178947904 23 33 3 178952072 38 45 3 178952085 35 45 3 178952088 34 45 ``` Looking at annotations ``` cat gene_PIK3CA.vcf |bio-vcf --eval [r.chr,r.pos,r.info.ann] |grep ENST00000263967|wc -l 30 ``` alternative ``` cat gene_PIK3CA.vcf |bio-vcf --eval '[r.chr,r.pos,r.info.ann]' --filter 'r.info.ann =~ /ENST00000263967/' --seval 's.dp' 3 178921407 T|synonymous_variant|LOW|PIK3CA|ENSG00000121879|transcript|ENST00000263967|protein_coding|5/21|c.889C>T|p.Leu297Leu|1046/9093|889/3207|297/1068|| 32 32 38 43 27 34 30 37 32 36 44 37 25 27 43 30 11 23 19 37 28 17 13 ... ``` Let's try and do the same with Mongo ``` { "rec": { "chr": "<%= rec.chrom %>", "pos": <%= rec.pos %>, "ref": "<%= rec.ref %>", "alt": "<%= rec.alt[0] %>", "dp": <%= rec.info.dp %>, "ann": '"<%= rec.info.ann %>"' } } ``` ```sh mongoimport --db PIK3CA --collection vcf --drop --file PIK3CA.json --jsonArray ``` ```ruby db.vcf.find({"rec.ann": /ENST00000263967/i }).count() 30 ``` ## Load results into Python ```sh guix package -i python2-pip export PYTHONPATH="/home/user/.guix-profile/lib/python2.7/site-packages" pip install --install-option="--prefix=$HOME/opt/python" pymongo export PYTHONPATH="/home/user/.guix-profile/lib/python2.7/site-packages:$HOME/opt/python/lib/python2.7/site-packages" ``` Now start python: ```python from pymongo import MongoClient client = MongoClient() db = client.test # cursor = db.restaurants.find() cursor = db.restaurants.find({"borough": "Manhattan"}) for document in cursor: print(document) print(document["cuisine"]) print(document["grades"][0]["score"]>10) ``` ## Exercise 1 Write a Python script which queries the PIK3CA VCF file for the annotation as in ```ruby db.vcf.find({"rec.ann": /ENST00000263967/i }).count() 30 ``` ## Exercise 2 Write a Python mongo script which queries the PIK3CA file for something similar to ```sh cat gene_PIK3CA.vcf |bio-vcf --sfilter-samples 2,3 --seval s.dp --sfilter "s.dp>7" ``` when the bio-vcf template is ```ruby { "rec": { "chr": "<%= rec.chrom %>", "pos": <%= rec.pos %>, "ref": "<%= rec.ref %>", "alt": "<%= rec.alt[0] %>", "dp": <%= rec.info.dp %>, "samples": [ <%= a = [] rec.each_sample { |s| a.push s.dp } a.join(',') %> ] } } ``` So output looks like ```ruby { "rec": { "chr": "3", "pos": 178916581, "ref": "T", "alt": "C", "dp": 2345, "samples": [ 11,11,21,20,27,10,16,17,19,15,18,20,16,9,18,22,6,2,6,9,8,7,7,10,11,12,4,9,7,9,8,10,7,18,8,7 ,7,4,11,4,8,8,8,14,13,23,13,11,12,3,10,27,31,16,12,1,3,4,15,10,20,8,4,0,25,2,10,9,13,20,17,14,25,15,19,16 ,29,13,10,7,4,5,1,1,2,26,17,16,8,4,5,14,14,6,5,0,5,5,11,10,17,8,5,20,9,16,5,21,14,5,4,3,13,7,0,9,5,12,0,2 ,9,14,2,4,7,1,15,7,14,12,4,14,16,26,7,22,5,4,7,10,11,14,19,25,11,2,28,25,29,30,23,30,35,33,32,27,4,30,25, 33,32,5,9,19,13,13,16,17,8,1,19,8,6,1,20,1,21,6,8,12,33,22,2,16,9,26,23 ] } } ``` Hint: the answer is 25 ```sh user@debian:~$ cat gene_PIK3CA.vcf |bio-vcf --sfilter-samples 2,3 --seval s.dp --sfilter "s.dp>7" bio-vcf 0.9.2 (biogem Ruby 2.3.0 with pcows) by Pjotr Prins 2015 Options: {:show_help=>false, :source=>"https://github.com/pjotrp/bioruby-vcf", :version=>"0.9.2 (Pjotr Prins)", :date=>"2016-04-11 12:11:27 +0200", :thread_lines=>40000, :timeout=>180, :sfilter_samples=>["2", "3"], :seval=>"s.dp", :skip_header=>true, :sfilter=>"s.dp>7"} 3 178916581 21 20 3 178916644 35 29 3 178916645 35 39 3 178916651 36 31 3 178916931 26 23 3 178917478 21 19 3 178919190 21 24 3 178921407 38 43 3 178921525 13 18 3 178921553 14 11 3 178922274 15 16 3 178922277 17 17 3 178922364 19 24 3 178927401 32 26 3 178927410 36 31 3 178927969 13 11 3 178928098 18 26 3 178936082 22 24 3 178936091 24 32 3 178938747 12 12 3 178941853 15 15 3 178947904 25 33 3 178952072 46 45 3 178952085 51 45 3 178952088 47 45 user@debian:~$ cat gene_PIK3CA.vcf |bio-vcf --sfilter-samples 2,3 --seval s.dp --sfilter "s.dp>7"|wc -l bio-vcf 0.9.2 (biogem Ruby 2.3.0 with pcows) by Pjotr Prins 2015 Options: {:show_help=>false, :source=>"https://github.com/pjotrp/bioruby-vcf", :version=>"0.9.2 (Pjotr Prins)", :date=>"2016-04-11 12:11:42 +0200", :thread_lines=>40000, :timeout=>180, :sfilter_samples=>["2", "3"], :seval=>"s.dp", :skip_header=>true, :sfilter=>"s.dp>7"} 25 ``` bio-vcf-0.9.5/doc/Using_RDF.md000066400000000000000000000120141400124230400157050ustar00rootroot00000000000000# Using bio-vcf with RDF bio-vcf can output many types of formats. In this exercise we will load a triple store (4store) with VCF data and do some queries on that. ## Install and start 4store ### On GNU Guix See https://github.com/pjotrp/guix-notes/blob/master/packages/4store.org ### On Debian Get root ```sh su apt-get install avahi-daemon apt-get install raptor-utils exit ``` As normal user ```sh guix package -i sparql-query curl ``` Initialize and start the server again as root (or another user) ``` su export PATH=/home/user/.guix-profile/bin:$PATH mkdir -p /var/lib/4store dbname=test 4s-backend-setup $dbname 4s-backend $dbname 4s-httpd -p 8000 $dbname ``` Try the web browser and point it to http://localhost:8000/status/ Open a new terminal as user. Generate rdf with bio-vcf template ```ruby =HEADER @prefix : . =BODY <% id = ['chr'+rec.chr,rec.pos,rec.alt].join('_') %> :<%= id %> :query_id "<%= id %>"; :chr "<%= rec.chr %>" ; :alt "<%= rec.alt.join("") %>" ; :pos <%= rec.pos %> . ``` so it looks like ``` :chrX_134713855_A :query_id "chrX_134713855_A"; :chr "X" ; :alt "A" ; :pos 134713855 . ``` and test with rapper using [gatk_exome.vcf](https://github.com/pjotrp/bioruby-vcf/blob/master/test/data/input/gatk_exome.vcf) ```sh cat gatk_exome.vcf |bio-vcf -v --template rdf_template.erb cat gatk_exome.vcf |bio-vcf -v --template rdf_template.erb > my.rdf rapper -i turtle my.rdf ``` Load into 4store (when no errors) ```bash rdf=my.rdf uri=http://localhost:8000/data/http://biobeat.org/data/$rdf curl -X DELETE $uri curl -T $rdf -H 'Content-Type: application/x-turtle' $uri 201 imported successfully This is a 4store SPARQL server ``` First SPARQL query ```sh SELECT ?id WHERE { ?id "X". } ``` ``` cat sparql1.rq |sparql-query "http://localhost:8000/sparql/" -p ┌──────────────────────────────────────────────┐ │ ?id │ ├──────────────────────────────────────────────┤ │ │ │ │ │ │ └──────────────────────────────────────────────┘ ``` A simple python query may look like ```python import requests import subprocess host = "http://localhost:8000/" query = """ SELECT ?s ?p ?o WHERE { ?s ?p ?o . } LIMIT 10 """ r = requests.post(host, data={ "query": query, "output": "text" }) # print r.url print r.text ``` renders ``` ?id ``` A working example if you are using the server http://guix.genenetwork.org and the correct PREFIX: ```python #! /usr/bin/env python import requests import subprocess host = "http://guix.genenetwork.org/sparql/" query = """ PREFIX : SELECT ?id ?chr ?pos ?alt WHERE { { ?id :chr "X" . } UNION { ?id :chr "1" . } ?id :chr ?chr . ?id :alt ?alt . ?id :pos ?pos . FILTER (?pos > 107911705) . } """ r = requests.post(host, data={ "query": query, "output": "text" }) print r.text ``` ## EBI EBI SPARQL has some advanced examples of queries, such as ``` https://www.ebi.ac.uk/rdf/services/ensembl/sparql PREFIX rdf: PREFIX rdfs: PREFIX dcterms: PREFIX dc: PREFIX obo: PREFIX skos: PREFIX sio: PREFIX faldo: PREFIX identifiers: PREFIX ensembl: PREFIX ensembltranscript: PREFIX ensemblexon: PREFIX ensemblprotein: PREFIX ensemblterms: SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location { ?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ; a ?type; dc:identifier ?id . OPTIONAL { ?transcript faldo:location ?location . ?location faldo:begin [faldo:position ?begin] . ?location faldo:end [faldo:position ?end ] . ?location faldo:reference ?reference . } OPTIONAL {?type rdfs:label ?typeLabel} } ``` See https://www.ebi.ac.uk/rdf/services/ensembl/sparql # Exercise Today's exercise is to create a graph using bio-vcf and/or a small program using RDF triples and define a SPARQL query. The more interesting the graph/SPARQL the better. bio-vcf-0.9.5/doc/pcows.org000066400000000000000000000050611400124230400154530ustar00rootroot00000000000000* Parallel copy-on-write streaming (PCOWS) Copy-on-write can be offered by an operating system to provide efficient parallelisation for streaming operations typical in biology where chunks of data can be processed independently from the same starting point. PCOWS compares to a regular thread pool with the difference that data is not communicated through messages or pipes, but simply through memory. The only catch is that PCOWS threads can not easily communicate back. The Ruby parallel gem communicates back through pipes but that means the main thread can not proceed until all the pipes complete. PCOWS was first explored in the bio-ruby VCF tool (bio-vcf 0.7 series) and then replaced by the parallel gem (bio-vcf 0.8 series). Performance, unfortunately, deteriorated to the extent that PCOWS got retrofitted. PCOWS basically reads a file and chunks it on the main thread. Every chunk gets fed to a copy-on-write version of the Ruby interpreter which contains the full state up to the point of forking - this is an inexpensive procedure. Each chunk gets processed to a file. The main thread tracks these files and issues a separate thread for harvesting the ordered files so each gets piped to STDOUT in order. The reader thread tracks This means the reader thread is only held up by the number of allowed forks running at a time. Based on this description the interface can be expressed as a reader creating chunks of state that get passed on to a chunk processor named 'run' which gets a callback 'func'. Every time a chunk gets processed the reader checks the size of the thread pool and also checks whether output has become available. The threads communicate simply through a file. Each thread writes to STDOUT which has been redirected to a temporary file with extension '.part'. When the thread is complete, the file gets renamed by removing the '.part'. Files that lack the '.part' get printed to the real STDOUT and deleted on completion. I.e.: 1. STDOUT for a worker is redirected to a tempfile with extension '.part' 2. Worker thread writes to STDOUT 3. On completion '.part' gets removed from the filename 4. The main thread checks the next file to be printed based on filenames 5. A print thread gets invoked 6. The print thread removes the file The only communication between PCOW threads and the main running thread is therefore the renaming of the temporary file. This will also work on network mounted systems. For performance it can make a difference to use a fast disk for temporary files, though the Linux file caching will make it likely that buffers are still in RAM. bio-vcf-0.9.5/features/000077500000000000000000000000001400124230400146565ustar00rootroot00000000000000bio-vcf-0.9.5/features/cli.feature000066400000000000000000000075061400124230400170120ustar00rootroot00000000000000@cli Feature: Command-line interface (CLI) bio-vcf has a powerful command line interface. Here we regression test features. Scenario: Test the info filter using dp Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --filter 'r.info.dp>100'" Then I expect the named output to match the named output "r.info.dp" Scenario: Test the info filter using dp and threads Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --num-threads 4 --filter 'r.info.dp>2'" Then I expect the named output to match the named output "thread4" in under 30 seconds Scenario: Test the info filter using dp and threads with lines Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --num-threads 4 --thread-lines 4 --filter 'r.info.dp>2'" Then I expect the named output to match the named output "thread4_4" in under 30 seconds Scenario: Test the sample filter using dp Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --sfilter 's.dp>20'" Then I expect the named output to match the named output "s.dp" Scenario: Test the include sample filter using dp Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --ifilter 's.dp>100' --seval s.dp" Then I expect the named output to match the named output "ifilter_s.dp" Scenario: Test the info eval using dp Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --eval 'r.info.dp'" Then I expect the named output to match the named output "eval_r.info.dp" Scenario: Test the sample eval using dp Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --seval 's.dp'" Then I expect the named output to match the named output "seval_s.dp" Scenario: Test the sample filter + eval using dp Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -i --sfilter 's.dp>10' --seval 's.dp'" Then I expect the named output to match the named output "sfilter_seval_s.dp" Scenario: Rewrite an info field Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf --rewrite rec.info[\'sample\']=\'XXXXX\'" Then I expect the named output to match the named output "rewrite.info.sample" Scenario: Test eval-once Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf --eval-once header.meta[\'GATKCommandLine\']" Then I expect the named output to match the named output "eval_once" Scenario: Test JSON output with header meta data Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf --template template/vcf2json_full_header.erb" Then I expect the named output to match the named output "vcf2json_full_header" Scenario: Test JSON output with header meta data and query samples Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf --template template/vcf2json_use_meta.erb" Then I expect the named output to match the named output "vcf2json_use_meta" Scenario: Test deadlock on failed filter with threads Given I have input file(s) named "test/data/input/multisample.vcf" When I execute "./bin/bio-vcf -q --timeout 4 --num-threads 4 --thread-lines 4 --filter 't.info.dp>2'" Then I expect an error and the named output to match the named output "thread4_4_failed_filter" in under 30 seconds Scenario: Test VCF with no records Given I have input file(s) named "test/data/input/empty.vcf" When I execute "./bin/bio-vcf --timeout=5" Then I expect no errors bio-vcf-0.9.5/features/diff_count.feature000066400000000000000000000022351400124230400203550ustar00rootroot00000000000000@diff Feature: Variant calling (filters) - diffing nucleotide counts Basic filtering happens on the command line with the --filter switch. To support somewhat more advanced features the following features are included. When diffing nucleotide counts we want to find out which nucleotide defines the tumor. The difference has to be larger than 0 and the relative difference is the max. When a threshold is set only those nucleotides are included which pass the threshold (i.e., no more than x supporting nucleotides in the reference). The advantage is that filtering is possible without actually looking at the rec.alt and rec.ref values, i.e., no assumptions are being made about the underlying nucleotides. Scenario: Diffing nucleotide counts Given normal and tumor counts [0,25,0,1] and [0,40,0,12] When I look for the difference Then I expect the diff to be [0,15,0,11] And I expect the defining tumor nucleotide to be "T" And I expect the tumor count to be 12 When I set an inclusion threshold for the reference Then I expect the diff for threshold 2 to be [0,0,0,11] And the relative diff to be [0,0,0,0.85] bio-vcf-0.9.5/features/filter.feature000066400000000000000000000011421400124230400175160ustar00rootroot00000000000000@filter Feature: Adding filters bio-vcf can add soft filters. Rather than removing failing items we can inject filter state into the FILTER field. To add state such as PASS or LowDepth simply use a filter and the --set-filter switch. If a filter already has state the new one is appended with a semi-colon. Scenario: Test the info filter using dp and threads Given I have input file(s) named "test/data/input/somaticsniper.vcf" When I execute "./bin/bio-vcf --add-filter PASS --filter 'r.normal.dp>5 and r.tumor.dp>7'" Then I expect the named output to match the named output "pass1" bio-vcf-0.9.5/features/multisample.feature000066400000000000000000000106161400124230400205730ustar00rootroot00000000000000@multi Feature: Multi-sample VCF Here we take a VCF line and parse the information for multiple named samples Scenario: When parsing a record Given the multi sample header line """ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 """ When I parse the header Given multisample vcf line """ 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522 """ When I parse the record Then I expect rec.valid? to be true Then I expect rec.chrom to contain "1" Then I expect rec.pos to contain 10321 Then I expect rec.ref to contain "C" And I expect multisample rec.alt to contain ["T"] And I expect rec.qual to be 106.30 And I expect rec.info.ac to be 5 And I expect rec.info.af to be 0.357 And I expect rec.info.dp to be 1537 And I expect rec.info['dp'] to be 1537 And I expect rec.info.readposranksum to be 0.815 And I expect rec.info['ReadPosRankSum'] to be 0.815 And I expect rec.info.fields to contain ["AC", "AF", "AN", "BASEQRANKSUM", "DP", "DELS", "FS", "HAPLOTYPESCORE", "MLEAC", "MLEAF", "MQ", "MQ0", "MQRANKSUM", "QD", "READPOSRANKSUM"] And I expect rec.sample['Original'].ad to be [189,25] And I expect rec.sample['Original'].gt to be "0/1" And I expect rec.sample['s3t2'].ad to be [167,26] And I expect rec.sample['s3t2'].dp to be 196 And I expect rec.sample['s3t2'].gq to be 20 And I expect rec.sample['s3t2'].pl to be [20,0,522] # And the nicer self resolving And I expect rec.sample.original.gt to be "0/1" And I expect rec.sample.s3t2.pl to be [20,0,522] # And the even better And I expect rec.original.gt? to be true And I expect rec.original.gt to be "0/1" And I expect rec.s3t2.pl to be [20,0,522] # Check for missing data And I expect test rec.missing_samples? to be false And I expect test rec.original? to be true # Special functions And I expect r.original? to be true And I expect r.original.gti? to be true And I expect r.original.gti to be [0,1] And I expect r.original.gti[1] to be 1 And I expect r.original.gts? to be true And I expect r.original.gts to be ["C","T"] And I expect r.original.gts[1] to be "T" Given multisample vcf line """ 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL ./. ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33 """ When I parse the record Then I expect rec.pos to contain 10723 Then I expect rec.valid? to be true And I expect rec.original? to be false And I expect rec.sample.s1t1? to be false And I expect rec.sample.s3t2? to be true And I expect rec.missing_samples? to be true # Phased genotype Given multisample vcf line """ 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL 0|1 ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33 """ When I parse the record Then I expect rec.pos to contain 10723 Then I expect rec.valid? to be true And I expect r.original? to be true And I expect r.original.gts? to be true And I expect r.original.gts to be ["C","G"] And I expect r.original.gts[0] to be "C" And I expect r.original.gts[1] to be "G" # INFO fields with matching tails Given multisample vcf line """ 1 10723 . C G 73.85 . AC=4;AF=0.667;CIEND=999;END=111;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL 0|1 ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33 """ When I parse the record Then I expect r.info.end to be 111 And I expect r.info.ciend to be 999 bio-vcf-0.9.5/features/sfilter.feature000066400000000000000000000040301400124230400177000ustar00rootroot00000000000000@sfilter Feature: Sample filters Bio-vcf supports sample filters, where every sample is evaluated independently, though they have the rec information (chrom, pos, info) available. Scenario: Example of a sample Given the VCF line """ 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL """ When I evaluate '0/0:6,0:6:3:0,3,33' Then I expect s.empty? to be false Then I expect s.dp? to be true Then I expect s.dp to be 6 And sfilter 's.dp>4' to be true # Scenario: Sample with missing data When I evaluate missing '0/0:6,0:.:3:0,3,33' Then I expect s.empty? to be false Then I expect s.dp? to be false Then I expect s.dp to be nil And sfilter 's.dp>4' to throw an error # Scenario: Sample with missing data with ignore missing set When I evaluate missing '0/0:6,0:.:3:0,3,33' with ignore missing Then I expect s.empty? to be false Then I expect s.dp? to be false Then I expect s.dp to be nil And sfilter 's.dp>4' to be false # Scenario: Missing sample When I evaluate empty './.' Then I expect s.empty? to be true Then I expect s.dp? to be false Then I expect s.dp to be nil And sfilter 's.dp>4' to throw an error # Scenario: Missing sample with ignore missing set When I evaluate empty './.' with ignore missing Then I expect s.empty? to be true Then I expect s.dp? to be false Then I expect s.dp to be nil And sfilter 's.dp>4' to be false # Scenario: Wrong field name in sample When I evaluate '0/0:6,0:6:3:0,3,33' Then I expect s.empty? to be false Then I expect s.dp? to be true Then I expect s.what? to throw an error And I expect s.what to throw an error # Scenario: Get other information for a sample When I evaluate '0/0:6,0:6:3:0,3,33' Then I expect r.chrom to be "1" And I expect r.alt to be ["G"] And I expect r.info.af to be 0.667 bio-vcf-0.9.5/features/somaticsniper.feature000066400000000000000000000071131400124230400211150ustar00rootroot00000000000000@sniper Feature: VCF for Somatic Sniper Here we take a VCF line and parse the information given by Somatic Sniper. At this position the reference contains: AAAGAAAAGAAAAA (12A,2G) At this position the tumor contains: AAAAACACAA (8A,2C) rec.alt contains variants C,G. rec.tumor.bcount reflects the contents of the tumor (8A,2C) so rec.tumor.bcount[rec.alt] reflects the actual number of variants in the tumor. The mapping quality in the BAM file is 37/37 and base quality is 55/60 in normal and tumor respectively. For the second scenario: At this position the reference contains: (15A) At this position the tumor contains: AAAAAAAAATATTA (13A, 3T) Scenario: When parsing a record Given the somatic sniper vcf line """ 1 27691244 . A C,G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/2:0/2:14:0,12,0,2:12,0,2,0:14:35:14:14,35:37:37,37:1:. 0/1:0/1:10:0,8,0,2:8,2,0,0:18:35:18:20,51:37:37,37:2:33 """ When I parse the record Then I expect rec.chrom to contain "1" Then I expect rec.pos to contain 27691244 Then I expect rec.ref to contain "A" And I expect rec.alt to contain ["C","G"] And I expect rec.tumor.dp to be 10 And I expect rec.tumor.dp4 to be [0,8,0,2] And I expect rec.tumor.bcount.to_ary to be [8,2,0,0] And I expect rec.tumor.bcount[rec.alt] to be [2,0] And I expect rec.tumor.bcount["G"] to be 0 And I expect rec.tumor.bcount[1] to be 2 And I expect rec.tumor.bcount[3] to be 0 And I expect rec.tumor.bcount.sum to be 2 And I expect rec.tumor.bcount.max to be 2 And I expect rec.tumor.bq.to_ary to be [20,51] And I expect rec.tumor.bq["G"] to be 51 And I expect rec.tumor.bq[1] to be 51 And I expect rec.tumor.bq.min to be 20 And I expect rec.tumor.bq.max to be 51 And I expect rec.tumor.amq.to_ary to be [37,37] And I expect rec.tumor.mq to be 37 And I expect rec.tumor.ss to be 2 And I expect rec.tumor.ssc to be 33 And I expect rec.normal.ssc to be nil # The following are additional functions And I expect rec.call_diff to be [-4,2,-2,0] And I expect rec.call_nuc to be "C" And I expect rec.call_tumor_count to be 2 And I expect rec.call_normal_count to be 0 And I expect rec.call_tumor_relative_count to be 1.0 Given the somatic sniper vcf line """ 1 27686841 . A T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:15:3,12,0,0:15,0,0,0:66:37:0:25:37:37:0:. 0/1:0/1:16:2,11,0,3:13,0,0,3:30:37:30:34,55:37:37,37:2:37 """ When I parse the record Then I expect rec.chrom to contain "1" Then I expect rec.pos to contain 27686841 Then I expect rec.ref to contain "A" And I expect rec.alt to contain one ["T"] And I expect rec.tumor.dp to be 16 And I expect rec.tumor.dp4 to be [2,11,0,3] And I expect rec.tumor.bcount.to_ary to be [13,0,0,3] And I expect rec.tumor.bcount[rec.alt] to be one [3] And I expect rec.tumor.bcount["G"] to be 0 And I expect rec.tumor.bcount["T"] to be 3 And I expect rec.tumor.bcount[1] to be 0 And I expect rec.tumor.bcount[3] to be 3 And I expect rec.tumor.bcount.sum to be 3 And I expect rec.tumor.bcount.max to be 3 And I expect rec.tumor.bq.to_ary to be [34,55] And I expect rec.tumor.bq["T"] to be 34 And I expect rec.tumor.bq[1] to be 55 And I expect rec.tumor.bq.min to be 34 And I expect rec.tumor.bq.max to be 55 And I expect rec.tumor.amq.to_ary to be [37,37] And I expect rec.tumor.mq to be 37 And I expect rec.tumor.ss to be 2 bio-vcf-0.9.5/features/step_definitions/000077500000000000000000000000001400124230400202245ustar00rootroot00000000000000bio-vcf-0.9.5/features/step_definitions/bio-vcf_steps.rb000066400000000000000000000000001400124230400233020ustar00rootroot00000000000000bio-vcf-0.9.5/features/step_definitions/cli-feature.rb000066400000000000000000000017351400124230400227570ustar00rootroot00000000000000 Given /^I have input file\(s\) named "(.*?)"$/ do |arg1| @filenames = arg1.split(/,/) end When /^I execute "(.*?)"$/ do |arg1| @cmd = arg1 + ' < ' + @filenames[0] end # Then(/^I expect the named output to match the named output "(.*?)"$/) do |arg1| # RegressionTest::CliExec::exec(@cmd,arg1,ignore: '(##BioVcf|date|"version":)').should be_truthy # end # Then(/^I expect the named output to match the named output "([^"]*)" in under (\d+) seconds$/) do |arg1, arg2| # RegressionTest::CliExec::exec(@cmd,arg1,ignore: '(##BioVcf|date|"version":)',timeout: arg2.to_i).should be_truthy # end # Then(/^I expect an error and the named output to match the named output "(.*?)" in under (\d+) seconds$/) do |arg1,arg2| # RegressionTest::CliExec::exec(@cmd,arg1,ignore: '(FATAL|Waiting|from|vcf|Options|Final pid)',should_fail: true,timeout:arg2.to_i).should be_truthy # end # Then(/^I expect no errors$/) do # RegressionTest::CliExec::exec(@cmd, "empty").should be_truthy # end bio-vcf-0.9.5/features/step_definitions/diff_count.rb000066400000000000000000000030501400124230400226670ustar00rootroot00000000000000 Given(/^normal and tumor counts \[(\d+),(\d+),(\d+),(\d+)\] and \[(\d+),(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8| @normal = [arg1,arg2,arg3,arg4].map{|i|i.to_i} @tumor = [arg5,arg6,arg7,arg8].map{|i|i.to_i} end When(/^I look for the difference$/) do end Then(/^I expect the diff to be \[(\d+),(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4| expect(Variant.diff(@normal,@tumor)).to eq [arg1.to_i,arg2.to_i,arg3.to_i,arg4.to_i] end Then(/^the relative diff to be \[(\d+),(\d+)\.(\d+),(\d+),(\d+)\.(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5, arg6| res = [arg1.to_f,(arg2+'.'+arg3).to_f,arg4.to_i,(arg5+'.'+arg6).to_f] expect(Variant.relative_diff(@normal,@tumor)).to eq res end Then(/^I expect the defining tumor nucleotide to be "(.*?)"$/) do |arg1| expect(['A','C','G','T'][Variant.index(@normal,@tumor)]).to eq arg1 end Then(/^I expect the tumor count to be (\d+)$/) do |arg1| expect(@tumor[Variant.index(@normal,@tumor)]).to eq arg1.to_i end When(/^I set an inclusion threshold for the reference$/) do end Then(/^I expect the diff for threshold (\d+) to be \[(\d+),(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5| @t = arg1.to_i @t_diff = Variant.threshold_diff(@t,@normal,@tumor) expect(@t_diff).to eq [arg2.to_i,arg3.to_i,arg4.to_i,arg5.to_i] end Then(/^the relative diff to be \[(\d+),(\d+),(\d+),(\d+)\.(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5| res = [arg1.to_f,arg2.to_i,arg3.to_i,(arg4.to_s+'.'+arg5.to_s).to_f] expect(Variant.relative_threshold_diff(@t,@normal,@tumor)).to eq res end bio-vcf-0.9.5/features/step_definitions/multisample.rb000066400000000000000000000132011400124230400231020ustar00rootroot00000000000000Given(/^the multi sample header line$/) do |string| @header = VcfHeader.new @header.add(string) end When(/^I parse the header$/) do expect(@header.column_names.size).to eq 16 expect(@header.samples.size).to eq 7 expect(@header.samples).to eq ["Original", "s1t1", "s2t1", "s3t1", "s1t2", "s2t2", "s3t2"] end Given(/^multisample vcf line$/) do |string| @fields = VcfLine.parse(string.split(/\s+/).join("\t")) @rec1 = VcfRecord.new(@fields,@header) end Then(/^I expect multisample rec\.alt to contain \["(.*?)"\]$/) do |arg1| expect(@rec1.alt).to eq ["T"] end Then(/^I expect rec\.qual to be (\d+)\.(\d+)$/) do |arg1, arg2| expect(@rec1.qual).to eq 106.3 end Then(/^I expect rec\.info\.ac to be (\d+)$/) do |arg1| expect(@rec1.info.ac).to eq arg1.to_i end Then(/^I expect rec\.info\.af to be (\d+)\.(\d+)$/) do |arg1, arg2| expect(@rec1.info.af).to eq 0.357 end Then(/^I expect rec\.info\.dp to be (\d+)$/) do |arg1| expect(@rec1.info.dp).to eq 1537 end Then(/^I expect rec\.info\.readposranksum to be (\d+)\.(\d+)$/) do |arg1, arg2| expect(@rec1.info.readposranksum).to eq 0.815 end Then(/^I expect rec\.info\['dp'\] to be (\d+)$/) do |arg1| expect(@rec1.info['dp']).to eq 1537 end Then(/^I expect rec\.info\['ReadPosRankSum'\] to be (\d+)\.(\d+)$/) do |arg1, arg2| expect(@rec1.info['ReadPosRankSum']).to eq 0.815 end Then(/^I expect rec\.info\.fields to contain \["(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)", "(.*?)"\]$/) do |arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9, arg10, arg11, arg12, arg13, arg14, arg15| expect(@rec1.info.fields).to eq ["AC", "AF", "AN", "BASEQRANKSUM", "DP", "DELS", "FS", "HAPLOTYPESCORE", "MLEAC", "MLEAF", "MQ", "MQ0", "MQRANKSUM", "QD", "READPOSRANKSUM"] end Then(/^I expect rec\.sample\.original\.gt to be "(.*?)"$/) do |arg1| expect(@rec1.sample['Original'].gt).to eq "0/1" end Then(/^I expect rec\.original\.gt to be "(.*?)"$/) do |arg1| expect(@rec1.original.gt).to eq "0/1" end Then(/^I expect rec\.sample\['Original'\]\.gt to be "(.*?)"$/) do |arg1| expect(@rec1.sample['Original'].gt).to eq "0/1" end Then(/^I expect rec\.sample\['Original'\]\.ad to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec1.sample['Original'].ad).to eq [189,25] end Then(/^I expect rec\.sample\['Original'\]\.gt to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec1.sample['Original'].gt).to eq "0/1" end Then(/^I expect rec\.sample\['s(\d+)t(\d+)'\]\.ad to be \[(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4| expect(@rec1.sample['s3t2'].ad).to eq [167,26] end Then(/^I expect rec\.sample\['s(\d+)t(\d+)'\]\.dp to be (\d+)$/) do |arg1, arg2, arg3| expect(@rec1.sample['s3t2'].dp).to eq 196 end Then(/^I expect rec\.sample\['s(\d+)t(\d+)'\]\.gq to be (\d+)$/) do |arg1, arg2, arg3| expect(@rec1.sample['s3t2'].gq).to eq 20 end Then(/^I expect rec\.sample\['s(\d+)t(\d+)'\]\.pl to be \[(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5| expect(@rec1.sample['s3t2'].pl).to eq [20,0,522] end Then(/^I expect rec\.sample\.original\.gt to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec1.sample.original.gt).to eq "0/1" end Then(/^I expect rec\.sample\.s(\d+)t(\d+)\.pl to be \[(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5| expect(@rec1.sample.s3t2.pl).to eq [20,0,522] end Then(/^I expect rec\.original\.gt to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec1.original.gt).to eq "0/1" end Then(/^I expect rec\.s(\d+)t(\d+)\.pl to be \[(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5| expect(@rec1.s3t2.pl).to eq [20,0,522] end Then(/^I expect test rec\.missing_samples\? to be false$/) do expect(@rec1.missing_samples?).to be false end Then(/^I expect test rec\.original\? to be true$/) do expect(@rec1.original?).to be true end Then(/^I expect rec\.missing_samples\? to be true$/) do expect(@rec1.missing_samples?).to be true end Then(/^I expect rec\.original\? to be true$/) do expect(@rec1.original?).to be true end Then(/^I expect rec\.original\? to be false$/) do expect(@rec1.original?).to eq false end Then(/^I expect rec\.sample\.s(\d+)t(\d+)\? to be false$/) do |arg1, arg2| expect(@rec1.sample.s1t1?).to eq false end Then(/^I expect rec\.sample\.s(\d+)t(\d+)\? to be true$/) do |arg1, arg2| expect(@rec1.sample.s3t2?).to eq true end Then(/^I expect rec\.valid\? to be true$/) do expect(@rec1.valid?).to eq true end Then(/^I expect r\.original\.gt\? to be true$/) do expect(@rec1.original.gt?).to be true end Then(/^I expect r\.original\? to be true$/) do expect(@rec1.original?).to be true end Then(/^I expect rec\.original\? to be true$/) do expect(@rec1.original?).to be true end Then(/^I expect rec\.original\.gt\? to be true$/) do expect(@rec1.original.gt?).to be true end Then(/^I expect r\.original\.gti\? to be true$/) do expect(@rec1.original.gti?).to eq true end Then(/^I expect r\.original\.gti to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec1.original.gti).to eq [arg1.to_i,arg2.to_i] end Then(/^I expect r\.original\.gti\[(\d+)\] to be (\d+)$/) do |arg1, arg2| expect(@rec1.original.gti[arg1.to_i]).to eq arg2.to_i end Then(/^I expect r\.original\.gts\? to be true$/) do expect(@rec1.original.gts?).to eq true end Then(/^I expect r\.original\.gts to be \["(.*?)","(.*?)"\]$/) do |arg1, arg2| expect(@rec1.original.gts).to eq [arg1,arg2] end Then(/^I expect r\.original\.gts\[(\d+)\] to be "(.*?)"$/) do |arg1, arg2| expect(@rec1.original.gts[arg1.to_i]).to eq arg2 end Then(/^I expect r\.info\.end to be (\d+)$/) do |arg1| expect(@rec1.info.end).to eq arg1.to_i end Then(/^I expect r\.info\.ciend to be (\d+)$/) do |arg1| expect(@rec1.info.ciend).to eq arg1.to_i end bio-vcf-0.9.5/features/step_definitions/sfilter.rb000066400000000000000000000100151400124230400222160ustar00rootroot00000000000000Given(/^the VCF line$/) do |string| @header = VcfHeader.new @header.add("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSample") @vcfline = string end When(/^I evaluate '([^']+)'$/) do |arg1| # concat VCF line with sample (arg1) @fields = VcfLine.parse((@vcfline.split(/\s+/)+[arg1]).join("\t")) @rec = VcfRecord.new(@fields,@header) p @rec @g = @rec.sample['Sample'] p @g expect(@g).not_to be nil @s = VcfSample::Sample.new(@rec,@g) @ignore_missing = false end Then(/^I expect s\.empty\? to be false$/) do expect(@s.empty?).to be false expect(@s.sfilter("s.empty?",do_cache: false)).to be false end Then(/^I expect s\.dp\? to be true$/) do p ['eval s.dp?',@s.eval("s.dp?",do_cache: false)] p ['eval s.dp',@s.eval("s.dp",do_cache: false)] p @g.dp p @s.dp p @s.sfilter("s.dp?",do_cache: false) expect(@s.eval("s.dp?",do_cache: false)).to be true end Then(/^I expect s\.dp to be (\d+)$/) do |arg1| # p @s.eval("s.dp") p :now p ['eval s.dp?',@s.eval("s.dp?",do_cache: false)] p ['eval s.dp',@s.eval("s.dp",do_cache: false)] expect(@s.eval("s.dp",do_cache: false)).to equal arg1.to_i end Then(/^sfilter 's\.dp>(\d+)' to be true$/) do |arg1| expect(@s.sfilter("dp>#{arg1}",do_cache: false)).to be true end When(/^I evaluate missing '([^']+)'$/) do |arg1| # concat VCF line with sample (arg1) @fields = VcfLine.parse((@vcfline.split(/\s+/)+[arg1]).join("\t")) @rec = VcfRecord.new(@fields,@header) p @rec @g = @rec.sample['Sample'] @s = VcfSample::Sample.new(@rec,@g) p @s expect(@s).not_to be nil @ignore_missing = false end Then(/^I expect s\.dp\? to be false$/) do expect(@s.eval("s.dp?",do_cache: false)).to be false end Then(/^I expect s\.dp to be nil$/) do expect(@s.eval("s.dp",ignore_missing_data: @ignore_missing, do_cache: false)).to be nil end Then(/^sfilter 's\.dp>(\d+)' to throw an error$/) do |arg1| expect { @s.eval("s.dp>#{arg1}",do_cache: false) }.to raise_error NoMethodError end Then(/^sfilter 's\.dp>(\d+)' to be false$/) do |arg1| expect(@s.sfilter("s.dp>#{arg1}",ignore_missing_data: @ignore_missing, do_cache: false)).to be false end When(/^I evaluate empty '\.\/\.'$/) do # concat VCF line with sample (arg1) @fields = VcfLine.parse((@vcfline.split(/\s+/)+['./.']).join("\t")) @rec = VcfRecord.new(@fields,@header) p @rec @g = @rec.sample['Sample'] @s = VcfSample::Sample.new(@rec,@g) p @s expect(@s).not_to be nil @ignore_missing = false end When(/^I evaluate missing '([^']+)' with ignore missing$/) do |arg1| # concat VCF line with sample (arg1) @fields = VcfLine.parse((@vcfline.split(/\s+/)+[arg1]).join("\t")) @rec = VcfRecord.new(@fields,@header) p @rec @g = @rec.sample['Sample'] @s = VcfSample::Sample.new(@rec,@g) p @s expect(@s).not_to be nil @ignore_missing = true end Then(/^I expect s\.empty\? to be true$/) do expect(@s.sfilter("s.empty?",do_cache: false)).to be true end Then(/^I expect s\.dp to throw an error$/) do # @s.instance_eval { undef :dp } p @s.eval("s.dp",do_cache: false) expect { @s.eval("s.dp",do_cache: false) }.to raise_error NoMethodError end When(/^I evaluate empty '\.\/\.' with ignore missing$/) do # concat VCF line with sample (arg1) @fields = VcfLine.parse((@vcfline.split(/\s+/)+['./.']).join("\t")) @rec = VcfRecord.new(@fields,@header) p @rec @g = @rec.sample['Sample'] @s = VcfSample::Sample.new(@rec,@g) p @s expect(@s).not_to be nil @ignore_missing = true end Then(/^I expect s\.what\? to throw an error$/) do expect { @s.eval("s.what?",do_cache: false) }.to raise_error NoMethodError end Then(/^I expect s\.what to throw an error$/) do expect { @s.eval("s.what",do_cache: false) }.to raise_error NoMethodError end Then(/^I expect r\.chrom to be "(.*?)"$/) do |arg1| expect(@s.eval("r.chrom",do_cache: false)).to eq "1" end Then(/^I expect r\.alt to be \["(.*?)"\]$/) do |arg1| expect(@s.eval("r.alt",do_cache: false)).to eq ["G"] end Then(/^I expect r\.info\.af to be (\d+)\.(\d+)$/) do |arg1, arg2| expect(@s.eval("r.info.af",do_cache: false)).to eq 0.667 end bio-vcf-0.9.5/features/step_definitions/somaticsniper.rb000066400000000000000000000073621400124230400234410ustar00rootroot00000000000000Given(/^the somatic sniper vcf line$/) do |string| @fields = VcfLine.parse(string.split(/\s+/).join("\t")) end When(/^I parse the record$/) do header = VcfHeader.new @rec = VcfRecord.new(@fields,header) end Then(/^I expect rec\.chrom to contain "(.*?)"$/) do |arg1| expect(@rec.chrom).to eq "1" end Then(/^I expect rec\.pos to contain (\d+)$/) do |arg1| expect(@rec.pos).to eq arg1.to_i end Then(/^I expect rec\.ref to contain "(.*?)"$/) do |arg1| expect(@rec.ref).to eq arg1 end Then(/^I expect rec\.alt to contain \["(.*?)","(.*?)"\]$/) do |arg1, arg2| expect(@rec.alt).to eq [arg1,arg2] end Then(/^I expect rec\.alt to contain one \["(.*?)"\]$/) do |arg1| expect(@rec.alt).to eq [arg1] end Then(/^I expect rec\.tumor\.dp to be (\d+)$/) do |arg1| expect(@rec.tumor.dp).to eq arg1.to_i end Then(/^I expect rec\.tumor\.dp(\d+) to be \[(\d+),(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4, arg5| expect(@rec.tumor.dp4).to eq [arg2.to_i,arg3.to_i,arg4.to_i,arg5.to_i] end Then(/^I expect rec\.tumor\.bcount.to_ary to be \[(\d+),(\d+),(\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4| expect(@rec.tumor.bcount.to_ary).to eq [arg1.to_i,arg2.to_i,arg3.to_i,arg4.to_i] end Then(/^I expect rec\.tumor\.bcount\[rec\.alt\] to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec.tumor.bcount[@rec.alt]).to eq [arg1.to_i,arg2.to_i] end Then(/^I expect rec\.tumor\.bcount\[rec\.alt\] to be one \[(\d+)\]$/) do |arg1| expect(@rec.tumor.bcount[@rec.alt]).to eq [arg1.to_i] end Then(/^I expect rec\.tumor\.bcount\["(.*?)"\] to be (\d+)$/) do |arg1, arg2| expect(@rec.tumor.bcount[arg1]).to eq arg2.to_i end Then(/^I expect rec\.tumor\.bcount\[(\d+)\] to be (\d+)$/) do |arg1, arg2| expect(@rec.tumor.bcount[arg1.to_i]).to eq arg2.to_i end Then(/^I expect rec\.tumor\.bcount\.sum to be (\d+)$/) do |arg1| expect(@rec.tumor.bcount.sum).to eq arg1.to_i end Then(/^I expect rec\.tumor\.bcount\.max to be (\d+)$/) do |arg1| expect(@rec.tumor.bcount.max).to eq arg1.to_i end Then(/^I expect rec\.tumor\.bq\.to_ary to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec.tumor.bq.to_ary).to eq [arg1.to_i,arg2.to_i] end Then(/^I expect rec\.tumor\.bq\["(.*?)"\] to be (\d+)$/) do |arg1, arg2| expect(@rec.tumor.bq[arg1]).to eq arg2.to_i end Then(/^I expect rec\.tumor\.bq\[(\d+)\] to be (\d+)$/) do |arg1, arg2| expect(@rec.tumor.bq[arg1.to_i]).to eq arg2.to_i end Then(/^I expect rec\.tumor\.bq\.min to be (\d+)$/) do |arg1| expect(@rec.tumor.bq.min).to eq arg1.to_i end Then(/^I expect rec\.tumor\.bq\.max to be (\d+)$/) do |arg1| expect(@rec.tumor.bq.max).to eq arg1.to_i end Then(/^I expect rec\.tumor\.amq.to_ary to be \[(\d+),(\d+)\]$/) do |arg1, arg2| expect(@rec.tumor.amq.to_ary).to eq [arg1.to_i,arg2.to_i] end Then(/^I expect rec\.tumor\.mq to be (\d+)$/) do |arg1| expect(@rec.tumor.mq).to eq arg1.to_i end Then(/^I expect rec\.tumor\.ss to be (\d+)$/) do |arg1| expect(@rec.tumor.ss).to eq arg1.to_i end Then(/^I expect rec\.tumor\.ssc to be (\d+)$/) do |arg1| expect(@rec.tumor.ssc).to be 33 end Then(/^I expect rec\.normal\.ssc to be nil$/) do expect(@rec.normal.ssc).to be nil end Then(/^I expect rec.call_diff to be \[(\-\d+),(\d+),(\-\d+),(\d+)\]$/) do |arg1, arg2, arg3, arg4| expect(@rec.call_diff).to eq [arg1.to_i,arg2.to_i,arg3.to_i,arg4.to_i] end Then(/^I expect rec.call_nuc to be "(.*?)"$/) do |arg1| expect(@rec.call_nuc).to eq arg1 end Then(/^I expect rec.call_tumor_count to be (\d+)$/) do |arg1| expect(@rec.call_tumor_count).to eq arg1.to_i end Then(/^I expect rec.call_normal_count to be (\d+)$/) do |arg1| expect(@rec.call_normal_count).to eq arg1.to_i end Then(/^I expect rec.call_tumor_relative_count to be (\d+)\.(\d+)$/) do |arg1, arg2| expect(@rec.call_tumor_relative_count).to eq (arg1.to_s+'.'+arg2.to_s).to_f end bio-vcf-0.9.5/features/step_definitions/vcf_header.rb000066400000000000000000000025111400124230400226360ustar00rootroot00000000000000Given(/^the VCF header lines$/) do |string| header = VcfHeader.new header.add string @vcf = header end When(/^I parse the VCF header$/) do end Then(/^I expect vcf\.columns to be \[CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT','NORMAL','TUMOR'\]$/) do expect(@vcf.column_names).to eq ['CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT','NORMAL','TUMOR'] end Then(/^I expect vcf\.fileformat to be "(.*?)"$/) do |arg1| expect(@vcf.fileformat).to eq arg1 end Then(/^I expect vcf\.fileDate to be "(.*?)"$/) do |arg1| expect(@vcf.fileDate).to eq arg1 end Then(/^I expect vcf.field\['fileDate'\] to be "(.*?)"$/) do |arg1| expect(@vcf.field['fileDate']).to eq arg1 end Then(/^I expect vcf\.phasing to be "(.*?)"$/) do |arg1| expect(@vcf.phasing).to eq arg1 end Then(/^I expect vcf\.reference to be "(.*?)"$/) do |arg1| expect(@vcf.reference).to eq arg1 end Then(/^I expect vcf\.format\['(\w+)'\] to be (\{[^}]+\})/) do |arg1,arg2| expect(@vcf.format[arg1].to_s).to eq arg2 end Then(/^I expect vcf\.info\['(\w+)'\] to be (\{[^}]+\})/) do |arg1,arg2| expect(@vcf.info[arg1].to_s).to eq arg2 end Then(/^I expect vcf\.meta to contain all header meta information$/) do m = @vcf.meta expect(m['fileformat']).to eq "VCFv4.1" expect(m['FORMAT']['DP']['Number']).to eq "1" expect(m.size).to be 9 end bio-vcf-0.9.5/features/support/000077500000000000000000000000001400124230400163725ustar00rootroot00000000000000bio-vcf-0.9.5/features/support/env.rb000066400000000000000000000005261400124230400175120ustar00rootroot00000000000000 $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib') require 'bio-vcf' require 'rspec/expectations' # Add the regression module if in the path (it can also be a gem) rootdir = File.dirname(__FILE__) + '/../..' $LOAD_PATH.unshift(rootdir+'/lib/regressiontest',rootdir+'/../regressiontest/lib') require 'regressiontest' include BioVcf bio-vcf-0.9.5/features/vcf_header.feature000066400000000000000000000035721400124230400203300ustar00rootroot00000000000000@meta Feature: Parsing VCF meta information from the header Take a header and parse that information as defined by the VCF standard. Scenario: When parsing a header line Given the VCF header lines """ ##fileformat=VCFv4.1 ##fileDate=20140121 ##phasing=none ##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR """ When I parse the VCF header Then I expect vcf.columns to be [CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT','NORMAL','TUMOR'] And I expect vcf.fileformat to be "VCFv4.1" And I expect vcf.fileDate to be "20140121" And I expect vcf.field['fileDate'] to be "20140121" And I expect vcf.phasing to be "none" And I expect vcf.reference to be "file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta" And I expect vcf.format['GT'] to be {"ID"=>"GT", "Number"=>"1", "Type"=>"String", "Description"=>"Genotype"} And I expect vcf.format['DP'] to be {"ID"=>"DP", "Number"=>"1", "Type"=>"Integer", "Description"=>"Total read depth"} And I expect vcf.format['DP4'] to be {"ID"=>"DP4", "Number"=>"4", "Type"=>"Integer", "Description"=>"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"} And I expect vcf.info['PM'] to be {"ID"=>"PM", "Number"=>"0", "Type"=>"Flag", "Description"=>"Variant is Precious(Clinical,Pubmed Cited)"}' And I expect vcf.meta to contain all header meta information Scenario: When parsing the header of somatic_sniper.vcf Do something bio-vcf-0.9.5/guix.scm000066400000000000000000000037161400124230400145270ustar00rootroot00000000000000;; To use this file to build HEAD of bio-vcf: ;; ;; guix build -f guix.scm ;; ;; To get a development container (emacs shell will work) ;; ;; rm Gemfile.lock # remove any dependencies ;; guix environment -C -l guix.scm ;; ruby ./bin/bio-vcf ;; ;; rake test # for testing ;; rake rdoc # for generating docs (use-modules ((guix licenses) #:prefix license:) (guix gexp) (guix packages) (guix git-download) (guix build-system ruby) (guix build-system trivial) (gnu packages ruby) (gn packages ruby) (srfi srfi-1) (ice-9 popen) (ice-9 rdelim)) (define %source-dir (dirname (current-filename))) (define %git-commit (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ))) (define-public bio-vcf-source (package (name "bio-vcf-source") (version (git-version "0.9.5" "HEAD" %git-commit)) (source (local-file %source-dir #:recursive? #t)) (build-system trivial-build-system) (propagated-inputs `(("ruby" ,ruby) ("ruby-rake" ,ruby-rake))) (native-inputs `(("ruby-cucumber" ,ruby-cucumber) )) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((target (string-append (assoc-ref %outputs "out") "/share"))) (write target) (mkdir-p target) #t)))) (synopsis "Smart VCF parser DSL") (description "Bio-vcf provides a @acronym{DSL, domain specific language} for processing the VCF format. Record named fields can be queried with regular expressions. Bio-vcf is a new generation VCF parser, filter and converter. Bio-vcf is not only very fast for genome-wide (WGS) data, it also comes with a filtering, evaluation and rewrite language and can output any type of textual data, including VCF header and contents in RDF and JSON.") (home-page "http://github.com/vcflib/bio-vcf") (license license:expat))) bio-vcf-source bio-vcf-0.9.5/lib/000077500000000000000000000000001400124230400136065ustar00rootroot00000000000000bio-vcf-0.9.5/lib/bio-vcf.rb000066400000000000000000000011621400124230400154600ustar00rootroot00000000000000# Please require your code below, respecting the naming conventions in the # bioruby directory tree. # # For example, say you have a plugin named bio-plugin, the only uncommented # line in this file would be # # require 'bio/bio-plugin/plugin' # # In this file only require other files. Avoid other source code. require 'bio-vcf/utils' require 'bio-vcf/vcf' require 'bio-vcf/vcfsample' require 'bio-vcf/vcfheader_line' require 'bio-vcf/vcfheader' require 'bio-vcf/vcfline' require 'bio-vcf/vcfgenotypefield' require 'bio-vcf/vcfrecord' require 'bio-vcf/variant' require 'bio-vcf/vcfstatistics' require 'bio-vcf/bedfilter' bio-vcf-0.9.5/lib/bio-vcf/000077500000000000000000000000001400124230400151335ustar00rootroot00000000000000bio-vcf-0.9.5/lib/bio-vcf/bedfilter.rb000066400000000000000000000020551400124230400174220ustar00rootroot00000000000000module BioVcf class BedFilter def initialize bedfilen require 'binary_search/native' # Parse Bed file and build up search array chrs = {} info = {} File.open(bedfilen).each_line { | line | (chr,start,stop,gene) = line.strip.split(/\t/)[0..3] chrs[chr] ||= [] chrs[chr].push(stop.to_i) info[chr+':'+stop] = [chr,start.to_i,stop.to_i,gene] } # Make sure chrs is sorted @chrs = {} chrs.each { | k,list | @chrs[k] = list.sort } @info = info end def contains(rec) stop_list = @chrs[rec.chrom] if stop_list pos = rec.pos stop = stop_list.bsearch { |bedstop| bedstop >= pos } if stop rinfo = @info[rec.chrom+':'+stop.to_s] raise "Unexpected error in BED record for #{rec.chrom}:#{stop} position" if rinfo == nil start = rinfo[1] if pos >= start # p [rec.chrom,rec.pos,rinfo] return rinfo end end end nil end end end bio-vcf-0.9.5/lib/bio-vcf/pcows.rb000066400000000000000000000221001400124230400166060ustar00rootroot00000000000000# Parallel copy-on-write streaming (PCOWS) require 'tempfile' class PCOWS RUNNINGEXT = 'part' # file extension def initialize(num_threads,chunk_size,name=File.basename(__FILE__),timeout=180,quiet=false,debug=false) num_threads = cpu_count() if not num_threads # FIXME: set to cpu_num by default # $stderr.print "Using ",num_threads,"threads \n" @num_threads = num_threads @chunk_size = chunk_size @pid_list = [] @name = name @timeout = timeout @quiet = quiet @debug = debug if @debug $stderr.print "PCOWS running in DEBUG MODE\n" end if multi_threaded @tmpdir = Dir::mktmpdir(@name+'_') end @last_output = 0 # counter @output_locked = false end # Feed the worker 'func and state' to COWS. Note that func is a # lambda closure so it can pick up surrounding scope at invocation # in addition to the data captured in 'state'. def submit_worker(func,state) pid = nil if multi_threaded count = @pid_list.size+1 fn = mktmpfilename(count) pid = fork do # ---- This is running a new copy-on-write process tempfn = fn+'.'+RUNNINGEXT STDOUT.reopen(File.open(tempfn, 'w+')) func.call(state).each { | line | print line } STDOUT.flush STDOUT.close # sleep 0.1 # f.flush # f.close # sleep 0.2 # interval to make sure we are done writing, # otherwise there may be misses at the end of a # block (maybe the f.close fixed it) FileUtils::mv(tempfn,fn) exit(0) end Process.detach(pid) else # ---- Single threaded: call in main process and output immediately func.call(state).each { | line | print line } end @pid_list << [ pid,count,fn ] return true end def submit_final_worker(func,state) @final_worker = true submit_worker(func,state) end # Make sure no more than num_threads are running at the same time - # this is achieved by checking the PID table and the running files # in the tmpdir def wait_for_worker_slot() return if single_threaded Timeout.timeout(@timeout) do printed_timeout_message = false while true # ---- count running pids running = @pid_list.reduce(0) do | sum, info | (pid,count,fn) = info if pid_or_file_running?(pid,fn) sum+1 else sum end end return if running < @num_threads if not printed_timeout_message $stderr.print "Waiting for slot (timeout=#{@timeout})\n" if not @quiet printed_timeout_message = true end sleep 0.1 end end end # ---- In this section the output gets collected and passed on to a # printer thread. This function makes sure the printing is # ordered and that no printers are running at the same # time. The printer thread should be doing as little processing # as possible. # # In this implementation type==:by_line will call func for # each line. Otherwise it is called once with the filename. def process_output(func=nil,type=:by_line, blocking=false) return if single_threaded output = lambda { |fn| if type == :by_line File.new(fn).each_line { |buf| print buf } else func.call(fn) end } if @output_locked # ---- is the other thread still running? We wait until it # is finished to start the next one (pid,count,fn) = @output_locked $stderr.print "Checking for output_lock on existing #{fn}\n" if not @quiet return if File.exist?(fn) # continue because thread still processing # Now we should remove the .keep file cleanup_keep_file(fn) @last_output += 1 # get next one in line @output_locked = false end # ---- process the next output chunk. After completion it # gets renamed to chunk.keep. This to avoid missing # output (if we unlink the file prematurely) if info = @pid_list[@last_output] (pid,count,fn) = info $stderr.print "Testing (#{@last_output}) for output file ",[info],"\n" if @debug if File.exist?(fn) # Yes! We have the next output, create outputter @output_locked = info $stderr.print "Set lock on ",[info],"\n" if not @quiet if not blocking $stderr.print "Processing output file #{fn} (non-blocking)\n" if not @quiet pid = fork do output.call(fn) # after finishing output move it to .keep FileUtils::mv(fn,fn+'.keep') exit(0) end Process.detach(pid) else $stderr.print "Processing output file #{fn} (blocking)\n" if not @quiet output.call(fn) FileUtils::mv(fn,fn+'.keep') end else sleep 0.2 end end end # Wait for a worker slot to appear. When working the pid is writing # a file with extension .part(ial). After completion the file is # renamed without .part and a slot is free. def wait_for_worker(info) (pid,count,fn) = info if pid_or_file_running?(pid,fn) $stderr.print "Waiting up to #{@timeout} seconds for pid=#{pid} to complete #{fn}\n" if not @quiet begin Timeout.timeout(@timeout) do while not File.exist?(fn) # wait for the result to appear sleep 0.2 return if not pid_or_file_running?(pid,fn) # worker is gone end end # Partial file should have been renamed: raise "FATAL: child process #{pid} appears to have crashed #{fn}" if not File.exist?(fn) $stderr.print "OK pid=#{pid}, processing starts of #{fn}\n" if not @quiet rescue Timeout::Error # Kill it to speed up exit Process.kill 9, pid Process.wait pid $stderr.print "FATAL: child process killed because it stopped responding, pid = #{pid}, fn = #{fn}, count = #{count}\n" $stderr.print "Bailing out" raise end end end # This is the final cleanup after the reader thread is done. All workers # need to complete. def wait_for_workers() return if single_threaded @pid_list.each do |info| wait_for_worker(info) end end def process_remaining_output() return if single_threaded $stderr.print "Processing remaining output...\n" if not @quiet while @output_locked sleep 0.2 process_output() # keep trying end @pid_list.each do |info| (pid,count,fn) = info while pid_or_file_running?(pid,fn) or File.exist?(fn) $stderr.print "Trying: ",[info],"\n" if not @quiet process_output(nil,:by_line,true) sleep 0.2 end end while @output_locked sleep 0.1 process_output(nil,:by_line,true) end cleanup_tmpdir() end def cleanup() @pid_list.each do |info| (pid,count,fn) = info if pid_running?(pid) $stderr.print "Killing child ",[info],"\n" begin Process.kill 9, pid Process.wait pid rescue Errno::ENOENT $stdout.puts "INFO: #{pidfile} did not exist: Errno::ENOENT" if not @quiet rescue Errno::ESRCH $stdout.puts "INFO: The process #{opid} did not exist: Errno::ESRCH" if not @quiet end end File.unlink(fn) if File.exist?(fn) cleanup_keep_file(fn,wait: false) tempfn = fn+'.'+RUNNINGEXT File.unlink(tempfn) if File.exist?(tempfn) end cleanup_tmpdir() end private def mktmpfilename(num,ext=nil) @tmpdir+sprintf("/%0.6d-",num)+@name+(ext ? '.'+ext : '') end def pid_or_file_running?(pid,fn) (pid && pid_running?(pid)) or File.exist?(fn+'.'+RUNNINGEXT) end def pid_running?(pid) begin fpid,status=Process.waitpid2(pid,Process::WNOHANG) rescue Errno::ECHILD, Errno::ESRCH return false end return true if nil == fpid && nil == status return ! (status.exited? || status.signaled?) end def single_threaded @num_threads == 1 end def multi_threaded @num_threads > 1 end def cpu_count begin return File.read('/proc/cpuinfo').scan(/^processor\s*:/).size if File.exist? '/proc/cpuinfo' # Actually, the JVM does not allow fork... return Java::Java.lang.Runtime.getRuntime.availableProcessors if defined? Java::Java rescue LoadError # Count on MAC return Integer `sysctl -n hw.ncpu 2>/dev/null` end $stderr.print "Could not determine number of CPUs" if not @quiet 1 end def cleanup_keep_file(fn, opts = { wait: true }) if not @debug keep = fn+'.keep' return if not opts[:wait] and !File.exist?(keep) $stderr.print "Trying to remove #{keep}\n" if not @quiet while true if File.exist?(keep) $stderr.print "Removing #{keep}\n" if not @quiet File.unlink(keep) break # forever loop end sleep 0.1 end #forever end end def cleanup_tmpdir if not @debug $stderr.print "Removing dir #{@tmpdir}\n" if not @quiet Dir.unlink(@tmpdir) if @tmpdir end end end bio-vcf-0.9.5/lib/bio-vcf/template.rb000066400000000000000000000026171400124230400173010ustar00rootroot00000000000000require 'erb' module Bio class Template def initialize fn raise "Can not find template #{fn}!" if not File.exist?(fn) parse(File.read(fn)) end def parse buf header = [] body = [] footer = [] where = :header buf.split("\n").each do | line | case where when :header next if line =~ /=HEADER/ if line =~ /=BODY/ body = [] where = :body next end header << line when :body if line =~ /=FOOTER/ footer = [] where = :footer next end body << line else footer << line end end if body == [] body = header header = [] end @erb_header = ERB.new(header.join("\n")) if header.size @erb_body = ERB.new(body.join("\n")) if body.size @erb_footer = ERB.new(footer.join("\n")) if footer.size end def result env @erb.result(env) end def header env if @erb_header @erb_header.result(env) else "" end end def body env if @erb_body @erb_body.result(env) else "" end end def footer env if @erb_footer @erb_footer.result(env) else "" end end end end bio-vcf-0.9.5/lib/bio-vcf/utils.rb000066400000000000000000000007431400124230400166240ustar00rootroot00000000000000module BioVcf module ConvertStringToValue def self::integer?(str) !!Integer(str) rescue false end def self::float?(str) !!Float(str) rescue false end def self::convert str if str =~ /,/ str.split(/,/).map { |item| convert(item) } else if integer?(str) str.to_i else if float?(str) str.to_f else str end end end end end end bio-vcf-0.9.5/lib/bio-vcf/variant.rb000066400000000000000000000017731400124230400171340ustar00rootroot00000000000000module BioVcf module Variant def Variant.diff normal,tumor tumor.each_with_index.map {|t,i| t-normal[i]} end def Variant.threshold_diff t,normal,tumor normal2,tumor2 = apply_threshold(t,normal,tumor) diff(normal2,tumor2) end def Variant.relative_diff normal,tumor d = diff(normal,tumor) total = tumor.each_with_index.map {|t,i| t+normal[i]} total.each_with_index.map {|t,i| (t==0 ? 0 : ((d[i].to_f/t)*100.0).round/100.0)} end def Variant.relative_threshold_diff t,normal,tumor normal2,tumor2 = apply_threshold(t,normal,tumor) relative_diff(normal2,tumor2) end def Variant.index normal,tumor rd = relative_diff(normal,tumor) max = rd.reduce(0){|mem,v| (v>mem ? v : mem) } rd.index(max) end def Variant.apply_threshold t,normal,tumor normal2 = normal.map{|v| (v>t ? 0 : v) } tumor2 = tumor.each_with_index.map{|v,i| (normal2[i]==0 ? 0 : v) } return normal2,tumor2 end end end bio-vcf-0.9.5/lib/bio-vcf/vcf.rb000066400000000000000000000000231400124230400162310ustar00rootroot00000000000000 module BioVcf end bio-vcf-0.9.5/lib/bio-vcf/vcffile.rb000066400000000000000000000027221400124230400171010ustar00rootroot00000000000000module BioVcf # This class abstracts a VCF file that can be iterated. # The VCF can be plain text or compressed with gzip # Note that files compressed with bgzip will not work, as thie ruby implementation of Zlib don't allow concatenated files class VCFfile def initialize(file: "", is_gz: true) @file = file @is_gz = is_gz end def parseVCFheader(head_line="") m=/##INFO=/.match(head_line) {:id=>m[1],:number=>m[2],:type=>m[3],:desc=>m[4]} end #Returns an enum that can be used as an iterator. def each return enum_for(:each) unless block_given? io = nil if @is_gz infile = open(@file) io = Zlib::GzipReader.new(infile) else io = File.open(@file) end header = BioVcf::VcfHeader.new io.each_line do |line| line.chomp! if line =~ /^##fileformat=/ header.add(line) next end if line =~ /^#/ header.add(line) next end fields = BioVcf::VcfLine.parse(line) rec = BioVcf::VcfRecord.new(fields,header) yield rec end end end endbio-vcf-0.9.5/lib/bio-vcf/vcfgenotypefield.rb000066400000000000000000000120201400124230400210100ustar00rootroot00000000000000module BioVcf MAXINT=100_000 class ValueError < Exception end module VcfValue def VcfValue::empty? v v == nil or v == '' or v == '.' end end # Helper class for a list of (variant) values, such as A,G. # The [] function does the hard work. You can pass in an index (integer) # or nucleotide which translates to an index. # (see ./features for examples) class VcfNucleotideCount4 def initialize alt,list @alt = alt @list = list.split(/,/).map{|i| i.to_i} end def [] idx if idx.kind_of?(Integer) # return a value @list[idx] elsif idx.kind_of?(String) # return a value @list[["A","C","G","T"].index(idx)] else idx.kind_of?(Array) # return a list of values idx.map { |nuc| idx2 = ["A","C","G","T"].index(nuc) # p [idx,nuc,idx2,@list] @list[idx2] } end end def to_ary @list end # Return the max value on the nucleotides in the list (typically rec.alt) def max list = @alt values = self[list] values.reduce(0){ |memo,v| (v>memo ? v : memo) } end def min list = @alt values = self[list] values.reduce(MAXINT){ |memo,v| (vmemo ? v : memo) } end def min @list.reduce(MAXINT){ |memo,v| (v in record, did you mean r.info.#{name}?\n" raise end end def method_missing(m, *args, &block) name = m.to_s if name =~ /\?$/ # test for valid sample return !VcfSample::empty?(@fields[@sample_index[name.chop]]) else @samples[name] ||= VcfGenotypeField.new(@fields[@sample_index[name]],@format,@header,@ref,@alt) end end end end bio-vcf-0.9.5/lib/bio-vcf/vcfheader.rb000066400000000000000000000124741400124230400174170ustar00rootroot00000000000000# This module parses the VCF header. A header consists of lines # containing fields. Most fields are of 'key=value' type and appear # only once. These can be retrieved with the find_field method. # # INFO, FORMAT and contig fields are special as they appear multiple times # and contain multiple key values (identified by an ID field). # To retrieve these call 'info' and 'format' functions respectively, # which return a hash on the contained ID. # # For the INFO and FORMAT fields a Ragel parser is used, mostly to # deal with embedded quoted fields. module BioVcf module VcfHeaderParser def VcfHeaderParser.get_column_names(lines) lines.each do | line | if line =~ /^#[^#]/ # the first line that starts with a single hash names = line.split names[0].sub!(/^#/,'') return names end end nil end def VcfHeaderParser.parse_field(line, debug) BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(line, debug: debug) end end class VcfHeader attr_reader :lines, :field def initialize(debug = false) @debug = debug @lines = [] @field = {} @meta = nil @cached_filter_index = {} end # Add a new field to the header def add line @lines += line.split(/\n/) end # Push a special key value list to the header def tag h h2 = h.dup [:show_help,:skip_header,:verbose,:quiet,:debug].each { |key| h2.delete(key) } info = h2.map { |k,v| k.to_s.capitalize+'='+'"'+v.to_s+'"' }.join(',') line = '##BioVcf=<'+info+'>' @lines.insert(-2,line) line end def version @version ||= lines[0].scan(/##fileformat=VCFv(\d+\.\d+)/)[0][0] end def column_names @column_names ||= VcfHeaderParser::get_column_names(@lines) end def columns @column ||= column_names.size end def printable_header_line(fields) fields.map { | field | if field == '#samples' samples else field end }.join("\t") end def samples @samples ||= if column_names.size > 8 column_names[9..-1] else [] end end def samples_index_array @all_samples_index ||= column_names[9..-1].fill{|i| i} end def num_samples @num_samples ||= ( samples == nil ? 0 : samples.size ) end def sample_index return @sample_index if @sample_index index = {} samples.each_with_index { |k,i| index[k] = i+9 ; index[k.downcase] = i+9 } @sample_index = index index end # Give a list of samples (by index and/or name) and return 0-based index values # The cache has to be able to hanle multiple lists - that is why it is a hash. def sample_subset_index list cached = @cached_filter_index[list] if cached l = cached else l = [] list = samples_index_array() if not list list.each { |i| value = begin Integer(i) rescue idx = samples.index(i) if idx != nil idx else raise "Unknown sample name '#{i}'" end end l << value } @cached_filter_index[list] = l end l end # Look for a line in the header with the field name and return the # value, otherwise return nil def find_field name return field[name] if field[name] @lines.each do | line | value = line.scan(/###{name}=(.*)/) if value[0] v = value[0][0] field[name] = v return v end end nil end # Look for all the lines that match the field name and return # a hash of hashes. An empty hash is returned when there are # no matches. def find_fields name res = {} @lines.each do | line | value = line.scan(/###{name}=<(.*)>/) if value[0] str = value[0][0] # p str v = VcfHeaderParser.parse_field(line,@debug) id = v['ID'] res[id] = v end end # p res res end def format find_fields('FORMAT') end def filter find_fields('FILTER') end def contig find_fields('contig') end def info find_fields('INFO') end def gatkcommandline find_fields('GATKCommandLine') end def meta return @meta if @meta res = { 'INFO' => {}, 'FORMAT' => {}, 'FILTER' => {}, 'contig' => {}, 'GATKCommandLine' => {} } @lines.each do | line | value = line.scan(/##(.*?)=(.*)/) if value[0] k,v = value[0] if k != 'FORMAT' and k != 'INFO' and k != 'FILTER' and k != 'contig' and k != 'GATKCommandLine' # p [k,v] res[k] = v end end end res['INFO'] = info() res['FORMAT'] = format() res['FILTER'] = filter() res['contig'] = contig() res['GATKCommandLine'] = gatkcommandline() # p [:res, res] @meta = res # cache values res end def method_missing(m, *args, &block) name = m.to_s value = find_field(name) return value if value raise "Unknown VCF header query '#{name}'" end end end bio-vcf-0.9.5/lib/bio-vcf/vcfheader_line.rb000066400000000000000000000611721400124230400204250ustar00rootroot00000000000000 # line 1 "gen_vcfheaderline_parser.rl" # Ragel lexer for VCF-header # # This is compact a parser/lexer for the VCF header format. Bio-vcf # uses the parser to generate meta information that can be output to # (for example) JSON format. The advantage of using ragel as a state # engine is that it allows for easy parsing of key-value pairs with # syntax checking and, for example, escaped quotes in quoted string # values. This ragel parser/lexer generates valid Ruby; it should be # fairly trivial to generate python/C/JAVA instead. Note that this # edition validates ID and Number fields only. Other fields are # dumped 'AS IS'. # # Note the .rb version is generated from ./ragel/gen_vcfheaderline_parser.rl # # by Pjotr Prins (c) 2014/2015 module BioVcf module VcfHeaderParser module RagelKeyValues def self.debug msg # nothing # $stderr.print "DEBUG: ",msg,"\n" end =begin # line 75 "gen_vcfheaderline_parser.rl" =end # line 38 "gen_vcfheaderline_parser.rb" class << self attr_accessor :_simple_lexer_actions private :_simple_lexer_actions, :_simple_lexer_actions= end self._simple_lexer_actions = [ 0, 1, 0, 1, 1, 1, 2, 1, 3, 1, 15, 1, 16, 2, 0, 1, 2, 4, 15, 2, 6, 15, 2, 7, 15, 2, 9, 16, 2, 10, 16, 2, 11, 16, 2, 12, 15, 2, 13, 16, 2, 14, 16, 3, 5, 8, 15, 6, 9, 10, 13, 11, 14, 16 ] class << self attr_accessor :_simple_lexer_key_offsets private :_simple_lexer_key_offsets, :_simple_lexer_key_offsets= end self._simple_lexer_key_offsets = [ 0, 0, 1, 2, 7, 8, 9, 10, 13, 26, 35, 49, 51, 53, 58, 60, 62, 62, 62, 64, 70, 72, 77, 80, 91, 101, 111, 121, 131, 141, 151, 161, 171, 181, 191, 201, 211, 221, 231, 241, 251, 261, 270, 275, 277, 279, 279, 281, 283, 283, 293, 303, 313, 322, 327, 329, 331, 331, 333, 335, 335, 345, 354, 360, 371, 381, 391, 401, 411, 421, 430, 438, 440, 445, 448, 458, 468, 478, 488, 498, 508, 517, 524, 526, 528, 533, 535, 537, 537, 537, 549, 559, 569, 579, 589, 599, 609, 619, 629, 639, 649, 659, 669, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700 ] class << self attr_accessor :_simple_lexer_trans_keys private :_simple_lexer_trans_keys, :_simple_lexer_trans_keys= end self._simple_lexer_trans_keys = [ 35, 35, 65, 70, 71, 73, 99, 76, 84, 61, 44, 60, 62, 67, 68, 73, 78, 86, 97, 108, 48, 57, 65, 90, 98, 122, 46, 61, 95, 48, 57, 65, 90, 97, 122, 34, 39, 44, 46, 60, 62, 43, 45, 48, 57, 65, 90, 97, 122, 34, 92, 34, 92, 34, 39, 44, 60, 62, 39, 92, 39, 92, 48, 57, 44, 46, 60, 62, 48, 57, 48, 57, 44, 60, 62, 48, 57, 44, 60, 62, 44, 46, 60, 62, 95, 48, 57, 65, 90, 97, 122, 46, 61, 95, 111, 48, 57, 65, 90, 97, 122, 46, 61, 95, 109, 48, 57, 65, 90, 97, 122, 46, 61, 95, 109, 48, 57, 65, 90, 97, 122, 46, 61, 95, 97, 48, 57, 65, 90, 98, 122, 46, 61, 95, 110, 48, 57, 65, 90, 97, 122, 46, 61, 95, 100, 48, 57, 65, 90, 97, 122, 46, 61, 76, 95, 48, 57, 65, 90, 97, 122, 46, 61, 95, 105, 48, 57, 65, 90, 97, 122, 46, 61, 95, 110, 48, 57, 65, 90, 97, 122, 46, 61, 95, 101, 48, 57, 65, 90, 97, 122, 46, 61, 79, 95, 48, 57, 65, 90, 97, 122, 46, 61, 95, 112, 48, 57, 65, 90, 97, 122, 46, 61, 95, 116, 48, 57, 65, 90, 97, 122, 46, 61, 95, 105, 48, 57, 65, 90, 97, 122, 46, 61, 95, 111, 48, 57, 65, 90, 97, 122, 46, 61, 95, 110, 48, 57, 65, 90, 97, 122, 46, 61, 95, 115, 48, 57, 65, 90, 97, 122, 46, 61, 95, 48, 57, 65, 90, 97, 122, 34, 39, 44, 60, 62, 34, 92, 34, 92, 39, 92, 39, 92, 46, 61, 95, 97, 48, 57, 65, 90, 98, 122, 46, 61, 95, 116, 48, 57, 65, 90, 97, 122, 46, 61, 95, 101, 48, 57, 65, 90, 97, 122, 46, 61, 95, 48, 57, 65, 90, 97, 122, 34, 39, 44, 60, 62, 34, 92, 34, 92, 39, 92, 39, 92, 46, 61, 68, 95, 48, 57, 65, 90, 97, 122, 46, 61, 95, 48, 57, 65, 90, 97, 122, 48, 57, 65, 90, 97, 122, 44, 46, 60, 62, 95, 48, 57, 65, 90, 97, 122, 46, 61, 95, 117, 48, 57, 65, 90, 97, 122, 46, 61, 95, 109, 48, 57, 65, 90, 97, 122, 46, 61, 95, 98, 48, 57, 65, 90, 97, 122, 46, 61, 95, 101, 48, 57, 65, 90, 97, 122, 46, 61, 95, 114, 48, 57, 65, 90, 97, 122, 46, 61, 95, 48, 57, 65, 90, 97, 122, 43, 45, 46, 65, 71, 82, 48, 57, 48, 57, 44, 60, 62, 48, 57, 44, 60, 62, 46, 61, 95, 101, 48, 57, 65, 90, 97, 122, 46, 61, 95, 114, 48, 57, 65, 90, 97, 122, 46, 61, 95, 115, 48, 57, 65, 90, 97, 122, 46, 61, 95, 105, 48, 57, 65, 90, 97, 122, 46, 61, 95, 111, 48, 57, 65, 90, 97, 122, 46, 61, 95, 110, 48, 57, 65, 90, 97, 122, 46, 61, 95, 48, 57, 65, 90, 97, 122, 34, 39, 44, 60, 62, 48, 57, 34, 92, 34, 92, 34, 39, 44, 60, 62, 39, 92, 39, 92, 44, 60, 62, 95, 45, 46, 48, 57, 65, 90, 97, 122, 46, 61, 95, 115, 48, 57, 65, 90, 97, 122, 46, 61, 95, 115, 48, 57, 65, 90, 97, 122, 46, 61, 95, 101, 48, 57, 65, 90, 97, 122, 46, 61, 95, 109, 48, 57, 65, 90, 97, 122, 46, 61, 95, 98, 48, 57, 65, 90, 97, 122, 46, 61, 95, 108, 48, 57, 65, 90, 97, 122, 46, 61, 95, 121, 48, 57, 65, 90, 97, 122, 46, 61, 95, 101, 48, 57, 65, 90, 97, 122, 46, 61, 95, 110, 48, 57, 65, 90, 97, 122, 46, 61, 95, 103, 48, 57, 65, 90, 97, 122, 46, 61, 95, 116, 48, 57, 65, 90, 97, 122, 46, 61, 95, 104, 48, 57, 65, 90, 97, 122, 73, 79, 76, 84, 69, 82, 82, 77, 65, 65, 84, 75, 67, 111, 109, 109, 97, 110, 100, 76, 105, 110, 101, 78, 70, 79, 111, 110, 116, 105, 103, 0 ] class << self attr_accessor :_simple_lexer_single_lengths private :_simple_lexer_single_lengths, :_simple_lexer_single_lengths= end self._simple_lexer_single_lengths = [ 0, 1, 1, 5, 1, 1, 1, 3, 7, 3, 6, 2, 2, 5, 2, 2, 0, 0, 0, 4, 0, 3, 3, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 2, 2, 0, 2, 2, 0, 4, 4, 4, 3, 5, 2, 2, 0, 2, 2, 0, 4, 3, 0, 5, 4, 4, 4, 4, 4, 3, 6, 0, 3, 3, 4, 4, 4, 4, 4, 4, 3, 5, 2, 2, 5, 2, 2, 0, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0 ] class << self attr_accessor :_simple_lexer_range_lengths private :_simple_lexer_range_lengths, :_simple_lexer_range_lengths= end self._simple_lexer_range_lengths = [ 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 4, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 0, 3, 3, 3, 3, 3, 3, 3, 1, 0, 0, 0, 0, 0, 0, 0, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ] class << self attr_accessor :_simple_lexer_index_offsets private :_simple_lexer_index_offsets, :_simple_lexer_index_offsets= end self._simple_lexer_index_offsets = [ 0, 0, 2, 4, 10, 12, 14, 16, 20, 31, 38, 49, 52, 55, 61, 64, 67, 68, 69, 71, 77, 79, 84, 88, 97, 105, 113, 121, 129, 137, 145, 153, 161, 169, 177, 185, 193, 201, 209, 217, 225, 233, 240, 246, 249, 252, 253, 256, 259, 260, 268, 276, 284, 291, 297, 300, 303, 304, 307, 310, 311, 319, 326, 330, 339, 347, 355, 363, 371, 379, 386, 394, 396, 401, 405, 413, 421, 429, 437, 445, 453, 460, 467, 470, 473, 479, 482, 485, 486, 487, 496, 504, 512, 520, 528, 536, 544, 552, 560, 568, 576, 584, 592, 595, 597, 599, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653 ] class << self attr_accessor :_simple_lexer_trans_targs private :_simple_lexer_trans_targs, :_simple_lexer_trans_targs= end self._simple_lexer_trans_targs = [ 2, 0, 3, 0, 4, 102, 110, 124, 127, 0, 5, 0, 6, 0, 7, 0, 8, 8, 132, 0, 24, 49, 60, 64, 74, 90, 97, 9, 9, 9, 0, 9, 10, 9, 9, 9, 9, 0, 11, 14, 8, 22, 8, 132, 18, 23, 23, 23, 0, 13, 17, 12, 13, 17, 12, 11, 14, 8, 8, 132, 0, 13, 16, 15, 13, 16, 15, 15, 12, 19, 0, 8, 20, 8, 132, 19, 0, 21, 0, 8, 8, 132, 21, 0, 8, 8, 132, 0, 8, 23, 8, 132, 23, 23, 23, 23, 0, 9, 10, 9, 25, 9, 9, 9, 0, 9, 10, 9, 26, 9, 9, 9, 0, 9, 10, 9, 27, 9, 9, 9, 0, 9, 10, 9, 28, 9, 9, 9, 0, 9, 10, 9, 29, 9, 9, 9, 0, 9, 10, 9, 30, 9, 9, 9, 0, 9, 10, 31, 9, 9, 9, 9, 0, 9, 10, 9, 32, 9, 9, 9, 0, 9, 10, 9, 33, 9, 9, 9, 0, 9, 10, 9, 34, 9, 9, 9, 0, 9, 10, 35, 9, 9, 9, 9, 0, 9, 10, 9, 36, 9, 9, 9, 0, 9, 10, 9, 37, 9, 9, 9, 0, 9, 10, 9, 38, 9, 9, 9, 0, 9, 10, 9, 39, 9, 9, 9, 0, 9, 10, 9, 40, 9, 9, 9, 0, 9, 10, 9, 41, 9, 9, 9, 0, 9, 42, 9, 9, 9, 9, 0, 43, 46, 8, 8, 132, 0, 42, 45, 44, 42, 45, 44, 44, 42, 48, 47, 42, 48, 47, 47, 9, 10, 9, 50, 9, 9, 9, 0, 9, 10, 9, 51, 9, 9, 9, 0, 9, 10, 9, 52, 9, 9, 9, 0, 9, 53, 9, 9, 9, 9, 0, 54, 57, 8, 8, 132, 0, 53, 56, 55, 53, 56, 55, 55, 53, 59, 58, 53, 59, 58, 58, 9, 10, 61, 9, 9, 9, 9, 0, 9, 62, 9, 9, 9, 9, 0, 63, 63, 63, 0, 8, 63, 8, 132, 63, 63, 63, 63, 0, 9, 10, 9, 65, 9, 9, 9, 0, 9, 10, 9, 66, 9, 9, 9, 0, 9, 10, 9, 67, 9, 9, 9, 0, 9, 10, 9, 68, 9, 9, 9, 0, 9, 10, 9, 69, 9, 9, 9, 0, 9, 70, 9, 9, 9, 9, 0, 71, 71, 73, 73, 73, 73, 72, 0, 72, 0, 8, 8, 132, 72, 0, 8, 8, 132, 0, 9, 10, 9, 75, 9, 9, 9, 0, 9, 10, 9, 76, 9, 9, 9, 0, 9, 10, 9, 77, 9, 9, 9, 0, 9, 10, 9, 78, 9, 9, 9, 0, 9, 10, 9, 79, 9, 9, 9, 0, 9, 10, 9, 80, 9, 9, 9, 0, 9, 81, 9, 9, 9, 9, 0, 82, 85, 8, 8, 132, 89, 0, 84, 88, 83, 84, 88, 83, 82, 85, 8, 8, 132, 0, 84, 87, 86, 84, 87, 86, 86, 83, 8, 8, 132, 89, 89, 89, 89, 89, 0, 9, 10, 9, 91, 9, 9, 9, 0, 9, 10, 9, 92, 9, 9, 9, 0, 9, 10, 9, 93, 9, 9, 9, 0, 9, 10, 9, 94, 9, 9, 9, 0, 9, 10, 9, 95, 9, 9, 9, 0, 9, 10, 9, 96, 9, 9, 9, 0, 9, 10, 9, 61, 9, 9, 9, 0, 9, 10, 9, 98, 9, 9, 9, 0, 9, 10, 9, 99, 9, 9, 9, 0, 9, 10, 9, 100, 9, 9, 9, 0, 9, 10, 9, 101, 9, 9, 9, 0, 9, 10, 9, 69, 9, 9, 9, 0, 103, 107, 0, 104, 0, 105, 0, 106, 0, 6, 0, 108, 0, 109, 0, 5, 0, 111, 0, 112, 0, 113, 0, 114, 0, 115, 0, 116, 0, 117, 0, 118, 0, 119, 0, 120, 0, 121, 0, 122, 0, 123, 0, 6, 0, 125, 0, 126, 0, 6, 0, 128, 0, 129, 0, 130, 0, 131, 0, 6, 0, 0, 0 ] class << self attr_accessor :_simple_lexer_trans_actions private :_simple_lexer_trans_actions, :_simple_lexer_trans_actions= end self._simple_lexer_trans_actions = [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 0, 7, 0, 0, 0, 0, 11, 0, 0, 9, 0, 9, 9, 0, 1, 1, 1, 0, 13, 1, 1, 3, 0, 0, 0, 0, 9, 9, 9, 0, 13, 1, 1, 3, 0, 0, 0, 0, 0, 11, 9, 0, 9, 9, 0, 0, 0, 11, 9, 9, 9, 0, 0, 9, 9, 9, 0, 16, 0, 16, 16, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 7, 0, 0, 0, 0, 0, 40, 0, 5, 0, 0, 0, 0, 40, 0, 0, 9, 9, 9, 0, 13, 1, 1, 3, 0, 0, 0, 13, 1, 1, 3, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 37, 0, 7, 0, 0, 0, 0, 0, 37, 0, 7, 0, 0, 0, 0, 0, 37, 0, 5, 0, 0, 0, 0, 37, 0, 0, 34, 34, 34, 0, 13, 1, 1, 3, 0, 0, 0, 13, 1, 1, 3, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 25, 0, 5, 0, 0, 0, 0, 25, 1, 1, 1, 25, 43, 0, 43, 43, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 5, 0, 0, 0, 0, 31, 1, 1, 1, 1, 1, 1, 1, 31, 0, 31, 22, 22, 22, 0, 0, 22, 22, 22, 0, 0, 7, 0, 0, 0, 0, 0, 28, 0, 7, 0, 0, 0, 0, 0, 28, 0, 7, 0, 0, 0, 0, 0, 28, 0, 7, 0, 0, 0, 0, 0, 28, 0, 7, 0, 0, 0, 0, 0, 28, 0, 7, 0, 0, 0, 0, 0, 28, 0, 5, 0, 0, 0, 0, 28, 0, 0, 9, 9, 9, 1, 0, 13, 1, 1, 3, 0, 0, 0, 0, 9, 9, 9, 0, 13, 1, 1, 3, 0, 0, 0, 0, 19, 19, 19, 0, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 25, 0, 7, 0, 0, 0, 0, 0, 25, 0, 7, 0, 0, 0, 0, 0, 25, 0, 7, 0, 0, 0, 0, 0, 25, 0, 7, 0, 0, 0, 0, 0, 25, 0, 7, 0, 0, 0, 0, 0, 25, 0, 7, 0, 0, 0, 0, 0, 25, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 7, 0, 0, 0, 0, 0, 31, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ] class << self attr_accessor :_simple_lexer_eof_actions private :_simple_lexer_eof_actions, :_simple_lexer_eof_actions= end self._simple_lexer_eof_actions = [ 0, 0, 0, 0, 0, 0, 0, 0, 47, 11, 0, 11, 11, 0, 11, 11, 11, 11, 11, 0, 11, 0, 0, 0, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 0, 40, 40, 40, 40, 40, 40, 37, 37, 37, 37, 0, 37, 37, 37, 37, 37, 37, 25, 25, 25, 0, 31, 31, 31, 31, 31, 31, 31, 31, 0, 0, 28, 28, 28, 28, 28, 28, 28, 0, 28, 28, 0, 28, 28, 28, 28, 0, 25, 25, 25, 25, 25, 25, 25, 31, 31, 31, 31, 31, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ] class << self attr_accessor :simple_lexer_start end self.simple_lexer_start = 1; class << self attr_accessor :simple_lexer_first_final end self.simple_lexer_first_final = 132; class << self attr_accessor :simple_lexer_error end self.simple_lexer_error = 0; class << self attr_accessor :simple_lexer_en_main end self.simple_lexer_en_main = 1; # line 79 "gen_vcfheaderline_parser.rl" # %% this just fixes syntax highlighting... def self.run_lexer(buf, options = {}) do_debug = (options[:debug] == true) $stderr.print "---> ",buf,"\n" if do_debug data = buf.unpack("c*") if(buf.is_a?(String)) eof = data.length values = [] stack = [] emit = lambda { |type, data, ts, p| # Print the type and text of the last read token # p ts,p $stderr.print "EMITTED: #{type}: #{data[ts...p].pack('c*')}\n" if do_debug values << [type,data[ts...p].pack('c*')] } error_code = nil # line 486 "gen_vcfheaderline_parser.rb" begin p ||= 0 pe ||= data.length cs = simple_lexer_start end # line 99 "gen_vcfheaderline_parser.rl" # line 495 "gen_vcfheaderline_parser.rb" begin _klen, _trans, _keys, _acts, _nacts = nil _goto_level = 0 _resume = 10 _eof_trans = 15 _again = 20 _test_eof = 30 _out = 40 while true _trigger_goto = false if _goto_level <= 0 if p == pe _goto_level = _test_eof next end if cs == 0 _goto_level = _out next end end if _goto_level <= _resume _keys = _simple_lexer_key_offsets[cs] _trans = _simple_lexer_index_offsets[cs] _klen = _simple_lexer_single_lengths[cs] _break_match = false begin if _klen > 0 _lower = _keys _upper = _keys + _klen - 1 loop do break if _upper < _lower _mid = _lower + ( (_upper - _lower) >> 1 ) if data[p].ord < _simple_lexer_trans_keys[_mid] _upper = _mid - 1 elsif data[p].ord > _simple_lexer_trans_keys[_mid] _lower = _mid + 1 else _trans += (_mid - _keys) _break_match = true break end end # loop break if _break_match _keys += _klen _trans += _klen end _klen = _simple_lexer_range_lengths[cs] if _klen > 0 _lower = _keys _upper = _keys + (_klen << 1) - 2 loop do break if _upper < _lower _mid = _lower + (((_upper-_lower) >> 1) & ~1) if data[p].ord < _simple_lexer_trans_keys[_mid] _upper = _mid - 2 elsif data[p].ord > _simple_lexer_trans_keys[_mid+1] _lower = _mid + 2 else _trans += ((_mid - _keys) >> 1) _break_match = true break end end # loop break if _break_match _trans += _klen end end while false cs = _simple_lexer_trans_targs[_trans] if _simple_lexer_trans_actions[_trans] != 0 _acts = _simple_lexer_trans_actions[_trans] _nacts = _simple_lexer_actions[_acts] _acts += 1 while _nacts > 0 _nacts -= 1 _acts += 1 case _simple_lexer_actions[_acts - 1] when 0 then # line 33 "gen_vcfheaderline_parser.rl" begin ts=p end when 1 then # line 34 "gen_vcfheaderline_parser.rl" begin emit.call(:value,data,ts,p) end when 2 then # line 38 "gen_vcfheaderline_parser.rl" begin emit.call(:kw,data,ts,p) end when 3 then # line 58 "gen_vcfheaderline_parser.rl" begin emit.call(:key_word,data,ts,p) end when 4 then # line 59 "gen_vcfheaderline_parser.rl" begin emit.call(:value,data,ts,p) end when 5 then # line 60 "gen_vcfheaderline_parser.rl" begin emit.call(:value,data,ts,p) end when 6 then # line 62 "gen_vcfheaderline_parser.rl" begin emit.call(:value,data,ts,p) end when 7 then # line 65 "gen_vcfheaderline_parser.rl" begin emit.call(:value,data,ts,p) end when 8 then # line 67 "gen_vcfheaderline_parser.rl" begin debug("ID FOUND") end when 9 then # line 67 "gen_vcfheaderline_parser.rl" begin error_code="Malformed ID" end when 10 then # line 68 "gen_vcfheaderline_parser.rl" begin error_code="Version" end when 11 then # line 69 "gen_vcfheaderline_parser.rl" begin error_code="Number" end when 12 then # line 70 "gen_vcfheaderline_parser.rl" begin debug("DATE FOUND") end when 13 then # line 70 "gen_vcfheaderline_parser.rl" begin error_code="Date" end when 14 then # line 71 "gen_vcfheaderline_parser.rl" begin error_code="GATK" end when 15 then # line 72 "gen_vcfheaderline_parser.rl" begin debug("KEY_VALUE found") end when 16 then # line 72 "gen_vcfheaderline_parser.rl" begin error_code="unknown key-value " end # line 647 "gen_vcfheaderline_parser.rb" end # action switch end end if _trigger_goto next end end if _goto_level <= _again if cs == 0 _goto_level = _out next end p += 1 if p != pe _goto_level = _resume next end end if _goto_level <= _test_eof if p == eof __acts = _simple_lexer_eof_actions[cs] __nacts = _simple_lexer_actions[__acts] __acts += 1 while __nacts > 0 __nacts -= 1 __acts += 1 case _simple_lexer_actions[__acts - 1] when 9 then # line 67 "gen_vcfheaderline_parser.rl" begin error_code="Malformed ID" end when 10 then # line 68 "gen_vcfheaderline_parser.rl" begin error_code="Version" end when 11 then # line 69 "gen_vcfheaderline_parser.rl" begin error_code="Number" end when 13 then # line 70 "gen_vcfheaderline_parser.rl" begin error_code="Date" end when 14 then # line 71 "gen_vcfheaderline_parser.rl" begin error_code="GATK" end when 16 then # line 72 "gen_vcfheaderline_parser.rl" begin error_code="unknown key-value " end # line 699 "gen_vcfheaderline_parser.rb" end # eof action switch end if _trigger_goto next end end end if _goto_level <= _out break end end end # line 100 "gen_vcfheaderline_parser.rl" raise "ERROR: "+error_code+" in "+buf if error_code begin res = {} # p values values.each_slice(2) do | a,b | $stderr.print '*',a,b if do_debug keyword = a[1] value = b[1] value = value.to_i if ['length','Epoch'].index(keyword) res[keyword] = value # p h[:value] if h[:name]==:identifier or h[:name]==:value or h[:name]==:string end rescue print "ERROR: " p values raise end $stderr.print(res,"\n") if do_debug res end end end end if __FILE__ == $0 gatkcommandline = < LINE1 h = {} s = gatkcommandline.strip # print s,"\n" result = BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: true) # h[result['ID']] = result # p result lines = < 13.0"> ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= LINES h = {} lines.strip.split("\n").each { |s| # print s,"\n" result = BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: true) h[result['ID']] = result p result } p h raise "ERROR" if h != {"HaplotypeScoreHigh"=>{"ID"=>"HaplotypeScoreHigh", "Description"=>"HaplotypeScore > 13.0"}, "GT"=>{"ID"=>"GT", "Number"=>"1", "Type"=>"String", "Description"=>"Genotype"}, "DP"=>{"ID"=>"DP", "Number"=>"1", "Type"=>"Integer", "Description"=>"Total read depth", "Extra"=>"Yes?"}, "DP4"=>{"ID"=>"DP4", "Number"=>"4", "Type"=>"Integer", "Description"=>"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"}, "PM"=>{"ID"=>"PM", "Number"=>"0", "Type"=>"Flag", "Description"=>"Variant is Precious(Clinical,Pubmed Cited)"}, "VP"=>{"ID"=>"VP", "Number"=>"1", "Type"=>"String", "Description"=>"Variation Property. Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf", "Source"=>"dbsnp", "Version"=>"138"}, "GENEINFO"=>{"ID"=>"GENEINFO", "Number"=>"1", "Type"=>"String", "Description"=>"Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:), and each pair is delimited by a vertical bar (|)"}, "CLNHGVS"=>{"ID"=>"CLNHGVS", "Number"=>".", "Type"=>"String", "Description"=>"Variant names from HGVS. The order of these variants corresponds to the order of the info in the other clinical INFO tags."}, "CLNHGVS1"=>{"ID"=>"CLNHGVS1", "Number"=>".", "Type"=>"String", "Description"=>"Variant names from \\\"HGVS\\\". The order of these 'variants' corresponds to the order of the info in the other clinical INFO tags."}, "XXXY12"=>{"ID"=>"XXXY12"}, "Y"=>{"ID"=>"Y", "length"=>59373566}} end # test bio-vcf-0.9.5/lib/bio-vcf/vcfline.rb000066400000000000000000000006311400124230400171060ustar00rootroot00000000000000module BioVcf module VcfLine # Split a line into fields and check size def VcfLine.parse line,expected_size=nil fields = line.strip.split(/\t/) raise "Unexpected line #{line}" if line.strip.size == 0 or fields.size < 6 raise "Expected #{expected_size} fields but got #{fields.size} in "+fields.to_s if expected_size and fields.size != expected_size fields end end end bio-vcf-0.9.5/lib/bio-vcf/vcfrdf.rb000066400000000000000000000065411400124230400167400ustar00rootroot00000000000000module BioVcf # This is some primarily RDF support - which may be moved to another gem # # Note that this functionality is superceded by the --template command! Though # this can be useful for one-liners. module VcfRdf def VcfRdf::header print < . @prefix rdfs: . @prefix dc: . @prefix hgnc: . @prefix doi: . @prefix db: . @prefix seq: . @prefix : . EOB end def VcfRdf::record id,rec,tags = "{}" id2 = [id,'ch'+rec.chrom,rec.pos,rec.alt.join('')].join('_') print <\] if s =~ /[^\\]\\[^\\]/ s2 = [] s.each_char.with_index { |c,i| res = c if i>0 and c == '\\' and s[i-1] != '\\' and s[i+1] !~ /^[uUtnr\\"]/ res = '\\' + c end # p [i,c,s[i+1],res] s2 << res } s = s2.join('') end s end def RDF::stringify_literal(literal) RDF::escape_string_literal(literal.to_s) end def RDF::quoted_stringify_literal(literal) '"' + stringify_literal(literal) + '"' end end module Turtle def Turtle::stringify_literal(literal) RDF::stringify_literal(literal) end def Turtle::identifier(id) raise "Illegal identifier #{id}" if id != Turtle::mangle_identifier(id) end # Replace letters/symbols that are not allowed in a Turtle identifier # (short hand URI). This should be the definite mangler and replace the # ones in bioruby-table and bio-exominer. Manglers are useful when using # data from other sources and trying to transform them into simple RDF # identifiers. def Turtle::mangle_identifier(s) id = s.strip.gsub(/[^[:print:]]/, '').gsub(/[#)(,]/,"").gsub(/[%]/,"perc").gsub(/(\s|\.|\$|\/|\\|\>)+/,"_") id = id.gsub(/\[|\]/,'') # id = URI::escape(id) id = id.gsub(/\|/,'_') id = id.gsub(/\-|:/,'_') if id != s # Don't want Bio depency in templates! # logger = Bio::Log::LoggerPlus.new 'bio-rdf' # logger.warn "\nWARNING: Changed identifier <#{s}> to <#{id}>" # $stderr.print "\nWARNING: Changed identifier <#{s}> to <#{id}>" end if not RDF::valid_uri?(id) raise "Invalid URI after mangling <#{s}> to <#{id}>!" end valid_id = if id =~ /^\d/ 'r' + id else id end valid_id # we certainly hope so! end end end bio-vcf-0.9.5/lib/bio-vcf/vcfrecord.rb000066400000000000000000000156001400124230400174370ustar00rootroot00000000000000module BioVcf class VcfRecordInfo def initialize s @info = s end def to_s if @h @h.map { |k,v| (v ? @original_key[k] + '=' + v : @original_key[k]) }.join(';') else @info end end def [] k # split_fields if not @h # /#{m}=(?[^;])/.@info kupper = k.upcase v = if @h @h[kupper] else @info =~ /[\A;]#{k}=([^;]+)/i value = $1 # p [m,value] # m = @info.match(/#{m.to_s.upcase}=(?[^;]+)/) slower! # value = m[:value] if value == nil split_fields # no option but to split @h[kupper] else value end end ConvertStringToValue::convert(v) end # Set INFO fields (used by --rewrite) def []= k, v split_fields if not @h kupper = k.upcase @h[kupper] = v @original_key[kupper] = k end def fields split_fields @h.keys end def method_missing(m, *args, &block) self[m.to_s] end private def split_fields return @h if @h @h = {} @original_key = {} @info.split(/;/).each do |f| k,v = f.split(/=/) kupper = k.upcase @h[kupper] = v @original_key[kupper] = k end end end module VcfRecordParser # Parse the format field into a Hash def VcfRecordParser.get_format s if s==$cached_sample_format_s $cached_sample_format else h = {} s.split(/:/).each_with_index { |v,i| h[v] = i } $cached_sample_format = h $cached_sample_format_s = s h end end def VcfRecordParser.get_info s VcfRecordInfo.new(s) end end module VcfRecordCall def call_diff Variant.diff(normal.bcount.to_ary,tumor.bcount.to_ary) end def call_nuc ['A','C','G','T'][index()] end # Get the GT when 0 is REF and >0 is ALT def get_gt(index) if index == 0 ref() else alt[index-1] end end def call_tumor_count tumor.bcount.to_ary[index()] end def call_tumor_relative_count Variant.relative_diff(normal.bcount.to_ary,tumor.bcount.to_ary)[index()] end def call_normal_count normal.bcount.to_ary[index()] end def index Variant.index(self.normal.bcount.to_ary,self.tumor.bcount.to_ary) end end class VcfRecord include VcfRecordCall attr_reader :header def initialize fields, header @fields = fields @header = header @sample_by_index = [] end def chrom @fields[0] end alias :chr :chrom def pos @pos ||= @fields[1].to_i end def ids @ids ||= @fields[2].split(';') end def id ids[0] end def ref @refs ||= @fields[3] end def alt @alt ||= @fields[4].split(/,/) end def qual @qual ||= @fields[5].to_f end def filter @filter ||= @fields[6] end def info @info ||= VcfRecordParser.get_info(@fields[7]) end def format @format ||= VcfRecordParser.get_format(@fields[8]) end # Return the first (single) sample (used in one sample VCF) def first @first ||= VcfGenotypeField.new(@fields[9],format,@header,ref,alt) end # Return the normal sample (used in two sample VCF) def normal first end # Return the tumor sample (used in two sample VCF) def tumor @tumor ||= VcfGenotypeField.new(@fields[10],format,@header,ref,alt) end # Return the sample as a named hash def sample @sample ||= VcfGenotypeFields.new(@fields,format,@header,ref,alt) end def sample_by_name name sample[name] end def sample_by_index i raise "Can not index sample on parameter <#{i}>" if not i.kind_of?(Integer) @sample_by_index[i] ||= VcfGenotypeField.new(@fields[i+9],format,@header,ref,alt) end # Walk the samples. list contains an Array of int (the index) def each_sample(list = nil) @header.sample_subset_index(list).each { |i| yield VcfSample::Sample.new(self,sample_by_index(i)) } end def samples list = [] each_sample { |s| list << s } list end def missing_samples? @fields[9..-1].each { |sample| return true if VcfSample::empty?(sample) } false end def valid? @fields.size == @header.column_names.size end def eval expr, ignore_missing_data: true, quiet: false begin if not respond_to?(:call_cached_eval) code = """ def call_cached_eval(rec,fields) r = rec #{expr} end """ self.class.class_eval(code) end res = call_cached_eval(self,@fields) if res.kind_of?(Array) res.join("\t") else res end rescue NoMethodError => e if not quiet $stderr.print "RECORD ERROR!\n" $stderr.print [@fields],"\n" $stderr.print expr,"\n" $stderr.print "To ignore this error use the -i switch!\n" end if ignore_missing_data $stderr.print e.message if not quiet return false else raise end end end def gfilter expr, ignore_missing_data: true, quiet: false begin if not respond_to?(:call_cached_filter) code = """ def call_cached_gfilter(rec,fields) r = rec #{expr} end """ self.class.class_eval(code) end res = call_cached_gfilter(self,@fields) if res.kind_of?(Array) res.join("\t") else res end rescue NoMethodError => e if not quiet $stderr.print "RECORD ERROR!\n" $stderr.print [@fields],"\n" $stderr.print expr,"\n" $stderr.print "To ignore this error use the -i switch!\n" end if ignore_missing_data $stderr.print e.message if not quiet return false else raise end end end def add_to_filter_field str filter = @fields[6] if not filter or filter == '.' or filter == 'PASS' filter = str else values = filter.split(/;/) if not values.include?(str) filter = filter +';'+str end end filter = '.' if filter == nil or filter == '' @fields[6] = filter filter end # Return the sample def method_missing(m, *args, &block) name = m.to_s if name =~ /\?$/ # Query for empty sample name @sample_index ||= @header.sample_index return !VcfSample::empty?(@fields[@sample_index[name.chop]]) else sample[name] end end end end bio-vcf-0.9.5/lib/bio-vcf/vcfsample.rb000066400000000000000000000116621400124230400174460ustar00rootroot00000000000000module BioVcf module VcfSample # Check whether a sample is empty (on the raw string value) def VcfSample::empty? s s==nil or s == './.' or s == '' or s[0..2]=='./.' or s[0..1] == '.:' end class Sample # Initialized sample with rec and genotypefield # # #0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, def initialize rec,genotypefield @rec = rec @sample = genotypefield @format = @sample.format @values = @sample.values end def empty? cache_empty ||= VcfSample::empty?(@sample.to_s) end def eval expr, ignore_missing_data: false, quiet: false, do_cache: true caching_eval :eval, :call_cached_eval, expr, ignore_missing_data: ignore_missing_data, quiet: quiet, do_cache: do_cache end def sfilter expr, ignore_missing_data: false, quiet: true, do_cache: true caching_eval :sfilter, :call_cached_sfilter, expr, ignore_missing_data: ignore_missing_data, quiet: quiet, do_cache: do_cache end def ifilter expr, ignore_missing_data: false, quiet: false, do_cache: true caching_eval :ifilter, :call_cached_ifilter, expr, ignore_missing_data: ignore_missing_data, quiet: quiet, do_cache: do_cache end def efilter expr, ignore_missing_data: false, quiet: false, do_cache: true caching_eval :efilter, :call_cached_efilter, expr, ignore_missing_data: ignore_missing_data, quiet: quiet, do_cache: do_cache end # Split GT into index values def gti v = fetch_values("GT") v = './.' if v == '.' #In case that you have a single missing value, make both as missing. v.split(/[\/\|]/).map{ |v| (v=='.' ? nil : v.to_i) } end def gtindex v = fetch_values("GT") return case v when nil then nil when '.' then nil when './.' then nil when '0/0' then 0 when '0/1' then 1 when '1/1' then 2 else raise "Unknown genotype #{v}" end end # Split GT into into a nucleode sequence def gts gti.map { |i| (i ? @rec.get_gt(i) : nil) } end def cache_method(name, &block) self.class.send(:define_method, name, &block) end def [] name if @format[name] v = fetch_values(name) return nil if VcfValue::empty?(v) return ConvertStringToValue::convert(v) end nil end def method_missing(m, *args, &block) name = m.to_s.upcase # p [:here,name,m ,@values] # p [:respond_to_call_cached_eval,respond_to?(:call_cached_eval)] if name =~ /\?$/ # test for valid field return !VcfValue::empty?(fetch_values(name.chop)) else if @format[name] cache_method(m) { v = fetch_values(name) return nil if VcfValue::empty?(v) ConvertStringToValue::convert(v) } self.send(m) else super(m, *args, &block) end end end private def fetch_values name n = @format[name] raise NoMethodError.new("Unknown sample field <#{name}>") if not n @values[n] # <-- save names with upcase! end def caching_eval method, cached_method, expr, ignore_missing_data: false, quiet: false, do_cache: true begin if do_cache if not respond_to?(cached_method) code = """ def #{cached_method}(rec,sample) r = rec s = sample #{expr} end """ self.class.class_eval(code) end self.send(cached_method,@rec,self) else # This is used for testing mostly print "WARNING: NOT CACHING #{method}\n" self.class.class_eval { undef :call_cached_eval } if respond_to?(:call_cached_eval) self.class.class_eval { undef :call_cached_sfilter } if respond_to?(:call_cached_sfilter) r = @rec s = @sample eval(expr) end rescue NoMethodError => e $stderr.print "\n#{method} trying to evaluate on an empty sample #{@sample.values.to_s}!\n" if not empty? and not quiet if not quiet $stderr.print [:format,@format,:sample,@values],"\n" $stderr.print [:filter,expr],"\n" end if ignore_missing_data $stderr.print e.message if not quiet and not empty? return false else raise NoMethodError.new(e.message + ". Can not evaluate empty sample data by default: test for s.empty? or use the -i switch!") end end end end end end bio-vcf-0.9.5/lib/bio-vcf/vcfstatistics.rb000066400000000000000000000011001400124230400203410ustar00rootroot00000000000000module BioVcf class VcfStatistics def initialize @count = 0 @ref_alt_count = {} end def add rec @count += 1 s = rec.ref+">"+rec.alt[0] @ref_alt_count[s] ||= 0 @ref_alt_count[s] += 1 end def print puts "## ==== Statistics ==================================" @ref_alt_count.sort_by {|k,v| v}.reverse.each do |k,v| printf k+"\t%d\t%2.0d%%\n",v,(v.to_f/@count*100).round end puts "Total\t#{@count}" puts "## ==================================================" end end end bio-vcf-0.9.5/lib/regressiontest.rb000066400000000000000000000005361400124230400172170ustar00rootroot00000000000000# Please require your code below, respecting the naming conventions in the # bioruby directory tree. # # For example, say you have a plugin named bio-plugin, the only uncommented # line in this file would be # # require 'bio/bio-plugin/plugin' # # In this file only require other files. Avoid other source code. require 'regressiontest/cli_exec' bio-vcf-0.9.5/lib/regressiontest/000077500000000000000000000000001400124230400166665ustar00rootroot00000000000000bio-vcf-0.9.5/lib/regressiontest/cli_exec.rb000066400000000000000000000063651400124230400210000ustar00rootroot00000000000000require 'fileutils' module RegressionTest DEFAULT_TESTDIR = "test/data/regression" # Regression test runner compares output in ./test/data/regression # (by default). The convention is to have a file with names .ref # (reference) and create .new # # You can add an :ignore regex option which ignores lines in the # comparson files matching a regex # # :timeout sets the time out for calling a system command # # :should_fail expects the system command to return a non-zero module CliExec FilePair = Struct.new(:outfn,:reffn) def CliExec::exec command, testname, options = {} # ---- Find .ref file fullname = DEFAULT_TESTDIR + "/" + testname basefn = if File.exist?(testname+".ref") || File.exist?(testname+"-stderr.ref") testname elsif File.exist?(fullname + ".ref") || File.exist?(fullname+"-stderr.ref") FileUtils.mkdir_p DEFAULT_TESTDIR fullname else raise "Can not find reference file for #{testname} - expected #{fullname}.ref" end std_out = FilePair.new(basefn + ".new", basefn + ".ref") std_err = FilePair.new(basefn + "-stderr.new", basefn + "-stderr.ref") files = [std_out,std_err] # ---- Create .new file cmd = command + " > #{std_out.outfn} 2>#{std_err.outfn}" $stderr.print cmd,"\n" exec_ret = nil if options[:timeout] && options[:timeout] > 0 Timeout.timeout(options[:timeout]) do begin exec_ret = Kernel.system(cmd) rescue Timeout::Error $stderr.print cmd, " failed to finish in under #{options[:timeout]}\n" return false end end else exec_ret = Kernel.system(cmd) end expect_fail = (options[:should_fail] != nil) if !expect_fail and exec_ret==0 $stderr.print cmd," returned an error\n" return false end if expect_fail and exec_ret $stderr.print cmd," did not return an error\n" return false end if options[:ignore] regex = options[:ignore] files.each do |f| outfn = f.outfn outfn1 = outfn + ".1" FileUtils.mv(outfn,outfn1) f1 = File.open(outfn1) f2 = File.open(outfn,"w") f1.each_line do | line | f2.print(line) if line !~ /#{regex}/ end f1.close f2.close FileUtils::rm(outfn1) end end # ---- Compare the two files files.each do |f| next unless File.exist?(f.reffn) return false unless compare_files(f.outfn,f.reffn,options[:ignore]) end return true end def CliExec::compare_files fn1, fn2, ignore = nil if not File.exist?(fn2) FileUtils::cp(fn1,fn2) true else cmd = "diff #{fn2} #{fn1}" $stderr.print cmd+"\n" return true if Kernel.system(cmd) == true # Hmmm. We have a different result. We are going to try again # because sometimes threads have not completed sleep 0.25 return true if Kernel.system(cmd) == true $stderr.print "If it is correct, execute \"cp #{fn1} #{fn2}\", and run again" false end end end end bio-vcf-0.9.5/ragel/000077500000000000000000000000001400124230400141325ustar00rootroot00000000000000bio-vcf-0.9.5/ragel/.gitignore000066400000000000000000000000051400124230400161150ustar00rootroot00000000000000*.rb bio-vcf-0.9.5/ragel/gen_vcfheaderline_parser.rl000066400000000000000000000231531400124230400215010ustar00rootroot00000000000000# Ragel lexer for VCF-header # # This is compact a parser/lexer for the VCF header format. Bio-vcf # uses the parser to generate meta information that can be output to # (for example) JSON format. The advantage of using ragel as a state # engine is that it allows for easy parsing of key-value pairs with # syntax checking and, for example, escaped quotes in quoted string # values. This ragel parser/lexer generates valid Ruby; it should be # fairly trivial to generate python/C/JAVA instead. Note that this # edition validates ID and Number fields only. Other fields are # dumped 'AS IS'. # # Note the .rb version is generated from ./ragel/gen_vcfheaderline_parser.rl # # by Pjotr Prins (c) 2014/2015 module BioVcf module VcfHeaderParser module RagelKeyValues def self.debug msg # nothing # $stderr.print "DEBUG: ",msg,"\n" end =begin %%{ machine simple_lexer; action mark { ts=p } action endquoted { emit.call(:value,data,ts,p) } action kw { emit.call(:kw,data,ts,p) } squote = "'"; dquote = '"'; not_squote_or_escape = [^'\\]; not_dquote_or_escape = [^"\\]; escaped_something = /\\./; ss = squote ( not_squote_or_escape | escaped_something )* >mark %endquoted squote; dd = dquote ( not_dquote_or_escape | escaped_something )* >mark %endquoted dquote; integer = ('+'|'-')?digit+; float = ('+'|'-')?digit+'.'digit+; assignment = '='; identifier = ( alnum (alnum|'.'|'_')* ); version = ( digit (alnum|'.'|'_'|'-')* ); str = (ss|dd)* ; boolean = '.'; date = str; key_word = ( ('Type'|'Description'|'Source'|identifier - ('ID'|'Number'|'length'|'Version'|'assembly'|'Date'|'CommandLineOptions')) >mark %{ emit.call(:key_word,data,ts,p) } ); any_value = ( str|( integer|float|boolean|identifier >mark %{ emit.call(:value,data,ts,p) } )); id_value = ( identifier >mark %{ emit.call(:value,data,ts,p) } ); version_value = ( str| ( version >mark %{ emit.call(:value,data,ts,p) } )); date_value = ( date ); gatk_value = ( str ); number_value = ( ( integer|boolean|'A'|'R'|'G' ) >mark %{ emit.call(:value,data,ts,p) } ); id_kv = ( ( ('ID'|'assembly') %kw '=' id_value ) %{ debug("ID FOUND") } @!{ error_code="Malformed ID"} ); version_kv = ( ( ('Version') %kw '=' version_value ) @!{ error_code="Version"} ); number_kv = ( ( ('Number'|'length') %kw '=' number_value ) @!{ error_code="Number"} ); date_kv = ( ( ('Date') %kw '=' date_value ) %{ debug("DATE FOUND") } @!{ error_code="Date"} ); gatk_kv = ( ( ('CommandLineOptions') %kw '=' gatk_value ) @!{ error_code="GATK"} ); key_value = ( id_kv | version_kv | date_kv | number_kv | gatk_kv | (key_word '=' any_value) ) %{ debug("KEY_VALUE found") } >mark @!{ error_code="unknown key-value " }; main := ( '##' ('FILTER'|'FORMAT'|'contig'|'INFO'|'ALT'|'GATKCommandLine') '=') (('<'|',') key_value )* '>'; }%% =end %% write data; # %% this just fixes syntax highlighting... def self.run_lexer(buf, options = {}) do_debug = (options[:debug] == true) $stderr.print "---> ",buf,"\n" if do_debug data = buf.unpack("c*") if(buf.is_a?(String)) eof = data.length values = [] stack = [] emit = lambda { |type, data, ts, p| # Print the type and text of the last read token # p ts,p $stderr.print "EMITTED: #{type}: #{data[ts...p].pack('c*')}\n" if do_debug values << [type,data[ts...p].pack('c*')] } error_code = nil %% write init; %% write exec; raise "ERROR: "+error_code+" in "+buf if error_code begin res = {} # p values values.each_slice(2) do | a,b | $stderr.print '*',a,b if do_debug keyword = a[1] value = b[1] value = value.to_i if ['length','Epoch'].index(keyword) res[keyword] = value # p h[:value] if h[:name]==:identifier or h[:name]==:value or h[:name]==:string end rescue print "ERROR: " p values raise end $stderr.print(res,"\n") if do_debug res end end end end if __FILE__ == $0 gatkcommandline = < LINE1 h = {} s = gatkcommandline.strip # print s,"\n" result = BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: true) # h[result['ID']] = result # p result lines = < 13.0"> ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= LINES h = {} lines.strip.split("\n").each { |s| # print s,"\n" result = BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: true) h[result['ID']] = result p result } p h raise "ERROR" if h != {"HaplotypeScoreHigh"=>{"ID"=>"HaplotypeScoreHigh", "Description"=>"HaplotypeScore > 13.0"}, "GT"=>{"ID"=>"GT", "Number"=>"1", "Type"=>"String", "Description"=>"Genotype"}, "DP"=>{"ID"=>"DP", "Number"=>"1", "Type"=>"Integer", "Description"=>"Total read depth", "Extra"=>"Yes?"}, "DP4"=>{"ID"=>"DP4", "Number"=>"4", "Type"=>"Integer", "Description"=>"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"}, "PM"=>{"ID"=>"PM", "Number"=>"0", "Type"=>"Flag", "Description"=>"Variant is Precious(Clinical,Pubmed Cited)"}, "VP"=>{"ID"=>"VP", "Number"=>"1", "Type"=>"String", "Description"=>"Variation Property. Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf", "Source"=>"dbsnp", "Version"=>"138"}, "GENEINFO"=>{"ID"=>"GENEINFO", "Number"=>"1", "Type"=>"String", "Description"=>"Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:), and each pair is delimited by a vertical bar (|)"}, "CLNHGVS"=>{"ID"=>"CLNHGVS", "Number"=>".", "Type"=>"String", "Description"=>"Variant names from HGVS. The order of these variants corresponds to the order of the info in the other clinical INFO tags."}, "CLNHGVS1"=>{"ID"=>"CLNHGVS1", "Number"=>".", "Type"=>"String", "Description"=>"Variant names from \\\"HGVS\\\". The order of these 'variants' corresponds to the order of the info in the other clinical INFO tags."}, "XXXY12"=>{"ID"=>"XXXY12"}, "Y"=>{"ID"=>"Y", "length"=>59373566}} end # test bio-vcf-0.9.5/ragel/generate.sh000077500000000000000000000002561400124230400162660ustar00rootroot00000000000000#! /bin/bash ragel -R gen_vcfheaderline_parser.rl [ $? -ne 0 ] && exit 1 ruby gen_vcfheaderline_parser.rb cp gen_vcfheaderline_parser.rb ../lib/bio-vcf/vcfheader_line.rb bio-vcf-0.9.5/template/000077500000000000000000000000001400124230400146535ustar00rootroot00000000000000bio-vcf-0.9.5/template/gatk_vcf2rdf.erb000066400000000000000000000016651400124230400177170ustar00rootroot00000000000000<% id = Turtle::mangle_identifier(['ch'+rec.chrom,rec.pos,rec.alt.join('')].join('_')) sample_num = 0 %> :<%= id %> :query_id "<%= id %>"; seq:chr "<%= rec.chrom %>" ; seq:pos <%= rec.pos %> ; seq:ref "<%= rec.ref %>" ; seq:alt "<%= rec.alt[0] %>" ; db:gatk true . <% rec.each_sample do | s | %> <% if not s.empty? sample_name = header.samples[sample_num] sample_id = id + '_' + Turtle::mangle_identifier(sample_name) sample_num += 1 if s.ad[0]+s.ad[1] != 0 alt_bias = (s.ad[1].to_f/(s.ad[0]+s.ad[1])).round(2) end %> :<%= sample_id %> :call_id :<%= id %> ; sample:name "<%= sample_name %>" ; sample:gt "<%= s.gt %>" ; <% s.gti.each do | index | %> sample:ad<%= index %> <%= s.ad[index] %> ; sample:gts<%= index %> "<%= s.gts[index] %>" ; <% end %> sample:dp <%= s.dp %> ; sample:alt_bias <%= alt_bias %> . <% end %> <% end %> bio-vcf-0.9.5/template/vcf2json.erb000066400000000000000000000005631400124230400171030ustar00rootroot00000000000000=HEADER <% require 'json' %> { "HEADER": { "options": <%= options.to_h.to_json %>, "files": <%= ARGV %>, "version": "<%= BIOVCF_VERSION %>" }, "BODY": [ =BODY { "seq:chr": "<%= rec.chrom %>", "seq:pos": <%= rec.pos %>, "seq:ref": "<%= rec.ref %>", "seq:alt": "<%= rec.alt[0] %>", "dp": <%= rec.info.dp %> }, =FOOTER ] } bio-vcf-0.9.5/template/vcf2json_full_header.erb000066400000000000000000000007601400124230400214340ustar00rootroot00000000000000=HEADER <% require 'json' %> { "HEADER": { "options": <%= options.to_h.to_json %>, "files": <%= ARGV %>, "version": "<%= BIOVCF_VERSION %>" }, "COLUMNS": <%= header.column_names.to_json %>, "META": <%= header.meta.to_json %>, "BODY": [ =BODY { "seq:chr": "<%= rec.chrom %>" , "seq:pos": <%= rec.pos %> , "seq:ref": "<%= rec.ref %>" , "seq:alt": "<%= rec.alt[0] %>" <% if rec.info.dp %> , "dp": <%= rec.info.dp %> <% end %> }, =FOOTER ] }bio-vcf-0.9.5/template/vcf2json_use_meta.erb000066400000000000000000000017111400124230400207610ustar00rootroot00000000000000=HEADER <% require 'json' %> { "HEADER": { "options":<%= options.to_h.to_json %>, "files": <%= ARGV %>, "version": "<%= BIOVCF_VERSION %>" }, "COLUMNS": <%= header.column_names.to_json %>, "META": <%= header.meta.to_json %>, "BODY": [ =BODY <% sample_num = 0 sample_name = nil sample_size = header.samples.size %> { "seq:chr": "<%= rec.chrom %>" , "seq:pos": <%= rec.pos %> , "seq:ref": "<%= rec.ref %>" , "seq:alt": "<%= rec.alt[0] %>" <% if rec.info.dp %> , "dp": <%= rec.info.dp %> <% end %>, "samples" : { <% rec.each_sample do |s| %> <% if not s.empty? sample_name = header.samples[sample_num] %> <%= (sample_num!=0 ? "," : "" ) %> <% sample_num += 1%> "<%= sample_name %>": { <% header.meta['FORMAT'].each_key do |k| %> "<%= k %>": <%= s[k].to_json %><%= (k==header.meta['FORMAT'].keys.last ? "" : "," ) %> <% end %> } <% end %> <% end %> } }, =FOOTER ] } bio-vcf-0.9.5/template/vcf2rdf.erb000066400000000000000000000005121400124230400166770ustar00rootroot00000000000000<% id = Turtle::mangle_identifier(['ch'+rec.chrom,rec.pos,rec.alt.join('')].join('_')) %> :<%= id %> :query_id "<%= id %>"; seq:chr "<%= rec.chrom %>" ; seq:pos <%= rec.pos %> ; seq:ref "<%= rec.ref %>" ; seq:alt "<%= rec.alt[0] %>" ; seq:dp <%= rec.info.dp %> ; db:vcf true . bio-vcf-0.9.5/template/vcf2rdf_header.erb000066400000000000000000000013441400124230400202130ustar00rootroot00000000000000=HEADER @prefix rdf: . @prefix rdfs: . @prefix dc: . @prefix hgnc: . @prefix doi: . @prefix seq: . @prefix db: . @prefix : . =BODY <% id = Turtle::mangle_identifier(['ch'+rec.chrom,rec.pos,rec.alt.join('')].join('_')) %> :<%= id %> :query_id "<%= id %>"; seq:chr "<%= rec.chrom %>" ; seq:pos <%= rec.pos %> ; seq:ref "<%= rec.ref %>" ; seq:alt "<%= rec.alt[0] %>" ; seq:dp <%= rec.info.dp %> ; db:vcf true . =FOOTERbio-vcf-0.9.5/test/000077500000000000000000000000001400124230400140175ustar00rootroot00000000000000bio-vcf-0.9.5/test/data/000077500000000000000000000000001400124230400147305ustar00rootroot00000000000000bio-vcf-0.9.5/test/data/input/000077500000000000000000000000001400124230400160675ustar00rootroot00000000000000bio-vcf-0.9.5/test/data/input/dbsnp.vcf000066400000000000000000001636021400124230400177050ustar00rootroot00000000000000##fileformat=VCFv4.0 ##fileDate=20140307 ##source=dbSNP ##dbSNP_BUILD_ID=138 ##reference=GRCh37.p10 ##phasing=partial ##variationPropertyDocumentationUrl=ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO=SubSNP->Batch.link_out"> ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO=5% minor allele frequency in each and all populations"> ##INFO=5% minor allele frequency in 1+ populations"> ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##INFO= ##INFO== 1% and for which 2 or more founders contribute to that minor allele frequency."> ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO 1 883516 rs267598747 G A . . RS=267598747;RSPOS=883516;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=NOC2L:26155;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.883516G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064926.2 1 891344 rs267598748 G A . . RS=267598748;RSPOS=891344;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=NOC2L:26155;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.891344G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064927.2 1 906168 rs267598759 G A . . RS=267598759;RSPOS=906168;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PLEKHN1:84069;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.906168G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064940.2 1 985955 rs199476396 G C . . RS=199476396;RSPOS=985955;dbSNPBuildID=136;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=AGRN:375790;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.985955G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=103320.0001;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1168:C1850792:254300:590;CLNDBN=Myasthenia\x2c_limb-girdle\x2c_familial;CLNACC=RCV000019902.26 1 1115553 rs267597918 C T . . RS=267597918;RSPOS=1115553;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=TTLL10:254173|TTLL10-AS1:100506376;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1115553C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064012.2 1 1119314 rs267597921 C G . . RS=267597921;RSPOS=1119314;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=TTLL10:254173;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1119314C>G;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064015.2 1 1167674 rs397514722 C T . . RS=397514722;RSPOS=1167674;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1167674C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0010;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=CN178404:615349:75496;CLNDBN=Ehlers-Danlos_syndrome\x2c_progeroid_type\x2c_2;CLNACC=RCV000054399.1 1 1167851 rs397514719 A G . . RS=397514719;RSPOS=1167851;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1167851A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0005;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054394.1 1 1167858 rs397514720 C T . . RS=397514720;RSPOS=1167858;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1167858C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0006;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054395.1 1 1168124 rs397514718 G A . . RS=397514718;RSPOS=1168124;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168124G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054392.1 1 1168277 rs397514723 G C . . RS=397514723;RSPOS=1168277;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168277G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0012;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=SPONDYLOEPIMETAPHYSEAL_DYSPLASIA_WITH_JOINT_LAXITY\x2c_TYPE_1\x2c_WITH_FRACTURES;CLNACC=RCV000054401.2 1 1168307 rs397514724 G A . . RS=397514724;RSPOS=1168307;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168307G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0013;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=SPONDYLOEPIMETAPHYSEAL_DYSPLASIA_WITH_JOINT_LAXITY\x2c_TYPE_1\x2c_WITH_FRACTURES;CLNACC=RCV000054402.1 1 1168352 rs397514717 C T . . RS=397514717;RSPOS=1168352;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168352C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:SNOMED_CT;CLNDSDBID=C0432243:271640:254100000;CLNDBN=Spondyloepimetaphyseal_dysplasia_with_joint_laxity;CLNACC=RCV000054391.1 1 1168583 rs397514721 T A . . RS=397514721;RSPOS=1168583;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=B3GALT6:126792|SDF4:51150;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1168583T>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=615291.0008;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=CN178404:615349:75496;CLNDBN=Ehlers-Danlos_syndrome\x2c_progeroid_type\x2c_2;CLNACC=RCV000054397.2 1 1245104 rs144003672 C A . . RS=144003672;RSPOS=1245104;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=ACAP3:116983|PUSL1:126789;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1245104C>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000059856.2 1 1248974 rs267597965 T A . . RS=267597965;RSPOS=1248974;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CPSF3L:54973;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1248974T>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064062.2 1 1469331 rs145324009 G A . . RS=145324009;RSPOS=1469331;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=ATAD3A:55210;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1469331G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000059865.2 1 1635335 rs201004006 G A . . RS=201004006;RSPOS=1635335;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=CDK11A:728642;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1635335G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064284.2 1 1905619 rs267598251 G A . . RS=267598251;RSPOS=1905619;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KIAA1751:85452;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1905619G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064400.2 1 1916905 rs267598254 G A . . RS=267598254;RSPOS=1916905;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KIAA1751:85452;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1916905G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064403.2 1 1916906 rs267598255 G A . . RS=267598255;RSPOS=1916906;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KIAA1751:85452;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1916906G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064404.2 1 1959075 rs121434580 A C . . RS=121434580;RSPOS=1959075;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=GABRD:2563;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959075A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0001;CLNSIG=255;CLNDSDB=MedGen;CLNDSDBID=C3150401;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5;CLNACC=RCV000017598.1 1 1959699 rs41307846 G A . . RS=41307846;RSPOS=1959699;dbSNPBuildID=127;SSR=0;SAO=1;VP=0x050260000000040116110100;GENEINFO=GABRD:2563;WGT=0;VC=SNV;PM;S3D;VLD;GNO;KGPhase1;KGPROD;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959699G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0002;CLNSIG=255|255|255;CLNDSDB=MedGen|MedGen|MedGen:OMIM;CLNDSDBID=C3150401|CN043549|C2751603:613060;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5|Epilepsy\x2c_juvenile_myoclonic_7|Epilepsy\x2c_idiopathic_generalized_10;CLNACC=RCV000017599.1|RCV000017600.1|RCV000022558.1;CAF=[0.9904,0.009642];COMMON=1 1 1961453 rs142619552 C T . . RS=142619552;RSPOS=1961453;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=GABRD:2563;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.1961453C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060029.2 1 2160299 rs387907304 C G . . RS=387907304;RSPOS=2160299;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160299C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0002;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000030817.20 1 2160305 rs387907306 G A,T . . RS=387907306;RSPOS=2160305;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1,2;CLNHGVS=NC_000001.10:g.2160305G>A,NC_000001.10:g.2160305G>T;CLNSRC=OMIM_Allelic_Variant,OMIM_Allelic_Variant;CLNORIGIN=.,.;CLNSRCID=164780.0004,164780.0005;CLNSIG=5,5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT,GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002,NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome,Shprintzen-Goldberg_syndrome;CLNACC=RCV000030819.24,RCV000030820.24 1 2160306 rs387907305 G A,T . . RS=387907305;RSPOS=2160306;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1,2;CLNHGVS=NC_000001.10:g.2160306G>A,NC_000001.10:g.2160306G>T;CLNSRC=OMIM_Allelic_Variant,OMIM_Allelic_Variant;CLNORIGIN=.,.;CLNSRCID=164780.0003,164780.0007;CLNSIG=5,5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT,GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002,NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome,Shprintzen-Goldberg_syndrome;CLNACC=RCV000030818.24,RCV000033005.24 1 2160308 rs397514590 C T . . RS=397514590;RSPOS=2160308;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160308C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0010;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000033008.24 1 2160309 rs397514589 C A . . RS=397514589;RSPOS=2160309;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160309C>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0009;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000033007.20 1 2160484 rs398122914 GTCCGACCGCTCC G . . RS=398122914;RSPOS=2160485;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=SKI:6497;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160485_2160496delTCCGACCGCTCC;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0008;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000033006.20 1 2160487 rs398122889 CGACCGCTCC C . . RS=398122889;RSPOS=2160488;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=SKI:6497;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160488_2160496delGACCGCTCC;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0006;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000030821.20 1 2160552 rs387907303 G A . . RS=387907303;RSPOS=2160552;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=SKI:6497;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2160552G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=164780.0001;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=NBK1277:C1321551:182212:2462:83092002;CLNDBN=Shprintzen-Goldberg_syndrome;CLNACC=RCV000030816.24 1 2337965 rs61752095 G C . . RS=61752095;RSPOS=2337965;RV;dbSNPBuildID=129;SSR=0;SAO=1;VP=0x050368000000000002110100;GENEINFO=PEX10:5192;WGT=0;VC=SNV;PM;PMC;S3D;SLO;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2337965G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602859.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM;CLNDSDBID=CN159233:614871;CLNDBN=Peroxisome_biogenesis_disorder_6B;CLNACC=RCV000007173.1 1 2340118 rs61750434 G A . . RS=61750434;RSPOS=2340118;RV;dbSNPBuildID=129;SSR=0;SAO=1;VP=0x050168000000000002110100;GENEINFO=PEX10:5192;WGT=0;VC=SNV;PM;PMC;SLO;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.2340118G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602859.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM;CLNDSDBID=CN159233:614871;CLNDBN=Peroxisome_biogenesis_disorder_6B;CLNACC=RCV000007174.1 1 2445510 rs267598457 G A . . RS=267598457;RSPOS=2445510;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2445510G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064619.2 1 2445511 rs267598458 G A . . RS=267598458;RSPOS=2445511;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2445511G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064620.2 1 2452272 rs267598460 C T . . RS=267598460;RSPOS=2452272;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2452272C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064622.2 1 2452273 rs267598461 C T . . RS=267598461;RSPOS=2452273;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PANK4:55229;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2452273C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064623.2 1 2938382 rs267598541 C T . . RS=267598541;RSPOS=2938382;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=ACTRT2:140625;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.2938382C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064708.2 1 3319357 rs267598556 G A . . RS=267598556;RSPOS=3319357;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3319357G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064723.2 1 3319550 rs397514744 C T . . RS=397514744;RSPOS=3319550;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3319550C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0005;CLNSIG=5;CLNDSDB=MedGen;CLNDSDBID=CN178850;CLNDBN=Dilated_cardiomyopathy_1LL;CLNACC=RCV000054522.1 1 3328865 rs397514742 A T . . RS=397514742;RSPOS=3328865;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.3328865A>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:Orphanet;CLNDSDBID=CN178849:615373:154:54260;CLNDBN=Left_ventricular_noncompaction_8;CLNACC=RCV000054518.1 1 3328870 rs267598557 C T . . RS=267598557;RSPOS=3328870;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3328870C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064724.2 1 3329208 rs397514743 A G . . RS=397514743;RSPOS=3329208;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.3329208A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:Orphanet;CLNDSDBID=CN178849:615373:154:54260;CLNDBN=Left_ventricular_noncompaction_8;CLNACC=RCV000054520.1 1 3331180 rs202115331 T C . . RS=202115331;RSPOS=3331180;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050260000000000002100100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3331180T>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0006;CLNSIG=5;CLNDSDB=MedGen;CLNDSDBID=CN178850;CLNDBN=Dilated_cardiomyopathy_1LL;CLNACC=RCV000054523.1 1 3334486 rs145632008 C A,T . . RS=145632008;RSPOS=3334486;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=2;CLNHGVS=NC_000001.10:g.3334486C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060177.2 1 3347452 rs201654872 G A . . RS=201654872;RSPOS=3347452;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=PRDM16:63976;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3347452G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=605557.0004;CLNSIG=5;CLNDSDB=MedGen;CLNDSDBID=CN178850;CLNDBN=Dilated_cardiomyopathy_1LL;CLNACC=RCV000054521.1 1 3548169 rs267598574 G A . . RS=267598574;RSPOS=3548169;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=WRAP73:49856;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3548169G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064742.2 1 3624269 rs267598580 A G . . RS=267598580;RSPOS=3624269;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=TP73:7161;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3624269A>G;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064748.2 1 3672076 rs267598583 G A . . RS=267598583;RSPOS=3672076;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CCDC27:148870;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3672076G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064751.2 1 3673309 rs267598584 C T . . RS=267598584;RSPOS=3673309;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CCDC27:148870;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3673309C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064752.2 1 3680269 rs139984517 G A . . RS=139984517;RSPOS=3680269;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CCDC27:148870;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3680269G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060186.2 1 3755581 rs139901107 G A . . RS=139901107;RSPOS=3755581;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CEP104:9731;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3755581G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060189.2 1 3765182 rs145420390 G A . . RS=145420390;RSPOS=3765182;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CEP104:9731;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.3765182G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060190.2 1 4832363 rs267598631 G T . . RS=267598631;RSPOS=4832363;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=AJAP1:55966;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.4832363G>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064801.2 1 5925224 rs398124290 G A . . RS=398124290;RSPOS=5925224;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.5925224G>A;CLNSRC=.|Emory_University;CLNORIGIN=.;CLNSRCID=.|3979;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081717.1 1 5935006 rs28940891 A G . . RS=28940891;RSPOS=5935006;RV;dbSNPBuildID=136;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5935006A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0004;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003571.1 1 5935033 rs398124289 T TGGAGC . . RS=398124289;RSPOS=5935033;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100200;GENEINFO=NPHP4:261734;WGT=0;VC=DIV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.5935034_5935038dupGGAGC;CLNSRC=.;CLNORIGIN=.;CLNSRCID=.;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081713.1 1 5940242 rs398124288 C T . . RS=398124288;RSPOS=5940242;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.5940242C>T;CLNSRC=.|Emory_University;CLNORIGIN=.;CLNSRCID=.|7428;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081709.1 1 5947454 rs137852919 G A . . RS=137852919;RSPOS=5947454;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5947454G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003569.1 1 5947463 rs137852918 C A . . RS=137852918;RSPOS=5947463;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5947463C>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003568.1 1 5947496 rs137852922 G A . . RS=137852922;RSPOS=5947496;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5947496G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0006;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1846979:606996:3156;CLNDBN=Senior-Loken_syndrome_4;CLNACC=RCV000003573.1 1 5964776 rs137852920 G A . . RS=137852920;RSPOS=5964776;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5964776G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1847013:606966:655;CLNDBN=Nephronophthisis_4;CLNACC=RCV000003570.1 1 5964848 rs137852923 G A . . RS=137852923;RSPOS=5964848;RV;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.5964848G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=607215.0007;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1846979:606996:3156;CLNDBN=Senior-Loken_syndrome_4;CLNACC=RCV000003574.1 1 6007278 rs398124287 T C . . RS=398124287;RSPOS=6007278;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6007278T>C;CLNSRC=.|Emory_University;CLNORIGIN=.;CLNSRCID=.|11436;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=not_provided;CLNACC=RCV000081703.1 1 6027450 rs200754878 C T . . RS=200754878;RSPOS=6027450;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000016100100;GENEINFO=NPHP4:261734;WGT=0;VC=SNV;PM;KGPhase1;KGPROD;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6027450C>T;CLNSRC=.;CLNORIGIN=.;CLNSRCID=.;CLNSIG=2;CLNDSDB=MedGen;CLNDSDBID=CN169374;CLNDBN=AllHighlyPenetrant;CLNACC=RCV000081720.1;CAF=[1,0];COMMON=0 1 6111773 rs267598678 C T . . RS=267598678;RSPOS=6111773;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KCNAB2:8514;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6111773C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064851.2 1 6151338 rs267598679 C T . . RS=267598679;RSPOS=6151338;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=KCNAB2:8514;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6151338C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064852.2 1 6170558 rs267598680 G A . . RS=267598680;RSPOS=6170558;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6170558G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064853.2 1 6172231 rs150855676 G A . . RS=150855676;RSPOS=6172231;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6172231G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060228.2 1 6211203 rs267598681 C A . . RS=267598681;RSPOS=6211203;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6211203C>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064854.2 1 6211204 rs267598682 A T . . RS=267598682;RSPOS=6211204;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CHD5:26038;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6211204A>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064855.2 1 6304465 rs267598684 G A . . RS=267598684;RSPOS=6304465;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=HES3:390992;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6304465G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064857.2 1 6511986 rs121908134 A C . . RS=121908134;RSPOS=6511986;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=ESPN:83715;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6511986A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=606351.0003;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Deafness\x2c_without_vestibular_involvement\x2c_autosomal_dominant;CLNACC=RCV000004670.1 1 6512061 rs121908135 G A . . RS=121908135;RSPOS=6512061;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=ESPN:83715;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6512061G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=606351.0004;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Deafness\x2c_without_vestibular_involvement\x2c_autosomal_dominant;CLNACC=RCV000004671.1 1 6512152 rs121908136 G A . . RS=121908136;RSPOS=6512152;dbSNPBuildID=132;SSR=0;SAO=1;VP=0x050060000000000002110100;GENEINFO=ESPN:83715;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6512152G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=606351.0005;CLNSIG=5;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Deafness\x2c_without_vestibular_involvement\x2c_autosomal_dominant;CLNACC=RCV000004672.1 1 6528438 rs202191898 C G,T . . RS=202191898;RSPOS=6528438;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000016110100;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;KGPhase1;KGPROD;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6528438C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0005;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054546.1;CAF=[0.9995,.,0.0004591];COMMON=0 1 6529456 rs397515456 G A . . RS=397515456;RSPOS=6529456;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6529456G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0004;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054547.1 1 6529504 rs63750315 A G . . RS=63750315;RSPOS=6529504;RV;dbSNPBuildID=130;SSR=0;SAO=1;VP=0x050268000000000002110100;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6529504A>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=611101.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C1970211:611067:206580;CLNDBN=Distal_spinal_muscular_atrophy\x2c_autosomal_recessive_4;CLNACC=RCV000001074.2 1 6530327 rs267598689 C T . . RS=267598689;RSPOS=6530327;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6530327C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064862.2 1 6530355 rs267598690 C T . . RS=267598690;RSPOS=6530355;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6530355C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064863.2 1 6531604 rs267598691 C T . . RS=267598691;RSPOS=6531604;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=PLEKHG5:57449;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6531604C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064864.2 1 6533111 rs397515455 C CGTCTTCA . . RS=397515455;RSPOS=6533111;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=PLEKHG5:57449;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6533112_6533118dupGTCTTCA;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054545.1 1 6537593 rs397515454 TG T . . RS=397515454;RSPOS=6537594;RV;dbSNPBuildID=136;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=PLEKHG5:57449;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.6537594delG;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=611101.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C3150897:613641:254334;CLNDBN=Charcot-Marie-Tooth_disease\x2c_recessive_intermediate_B;CLNACC=RCV000054544.1 1 6589228 rs145449783 G A . . RS=145449783;RSPOS=6589228;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=NOL9:79707;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6589228G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060234.2 1 6637073 rs148829212 C T . . RS=148829212;RSPOS=6637073;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=TAS1R1:80835;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6637073C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060235.2 1 6653500 rs137992292 G A . . RS=137992292;RSPOS=6653500;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=KLHL21:9903;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6653500G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064865.2 1 6706031 rs150959272 T A . . RS=150959272;RSPOS=6706031;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=DNAJC11:55735;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6706031T>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060237.2 1 6727837 rs267598695 G A . . RS=267598695;RSPOS=6727837;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=DNAJC11:55735;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.6727837G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064869.2 1 7723700 rs267598725 G A . . RS=267598725;RSPOS=7723700;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CAMTA1:23261;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7723700G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064902.2 1 7798488 rs267598727 C T . . RS=267598727;RSPOS=7798488;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CAMTA1:23261;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7798488C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064904.2 1 7811268 rs267598728 T C . . RS=267598728;RSPOS=7811268;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=CAMTA1:23261;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7811268T>C;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064905.2 1 7887271 rs139934930 C T . . RS=139934930;RSPOS=7887271;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=PER3:8863;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7887271C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060248.2 1 7887619 rs137949562 C T . . RS=137949562;RSPOS=7887619;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PER3:8863;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7887619C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064906.2 1 7895998 rs267598729 C T . . RS=267598729;RSPOS=7895998;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=PER3:8863;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.7895998C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064907.2 1 8022923 rs74315351 G A . . RS=74315351;RSPOS=8022923;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8022923G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602533.0003;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007481.1 1 8025408 rs137853051 G T . . RS=137853051;RSPOS=8025408;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8025408G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=602533.0007;CLNSIG=5;CLNDSDB=GeneReviews:MedGen;CLNDSDBID=NBK1223:C2751533;CLNDBN=Parkinson_disease\x2c_autosomal_recessive_early-onset\x2c_digenic\x2c_PINK1/DJ1;CLNACC=RCV000007485.1 1 8025485 rs74315353 G C . . RS=74315353;RSPOS=8025485;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8025485G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602533.0005;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007483.1 1 8044990 rs74315352 A C . . RS=74315352;RSPOS=8044990;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000040016110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;VLD;KGPhase1;KGPROD;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8044990A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=602533.0004;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007482.1;CAF=[0.9977,0.002296];COMMON=1 1 8045031 rs74315354 G A . . RS=74315354;RSPOS=8045031;dbSNPBuildID=131;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8045031G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=602533.0006;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007484.1 1 8045041 rs28938172 T C . . RS=28938172;RSPOS=8045041;dbSNPBuildID=133;SSR=0;SAO=1;VP=0x050260000000000002110100;GENEINFO=PARK7:11315;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.8045041T>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=602533.0002;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1223:C1853445:606324:2828;CLNDBN=Parkinson_disease_7;CLNACC=RCV000007480.1 1 8390585 rs138991605 C T . . RS=138991605;RSPOS=8390585;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;GENEINFO=SLC45A1:50651;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8390585C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060251.2 1 8390726 rs267598735 C T . . RS=267598735;RSPOS=8390726;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC45A1:50651;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8390726C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064913.2 1 8418710 rs115986998 G A . . RS=115986998;RSPOS=8418710;dbSNPBuildID=132;SSR=0;SAO=3;VP=0x050060000000150416100120;GENEINFO=RERE:473;WGT=0;VC=SNV;PM;VLD;G5;HD;KGPhase1;KGPROD;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8418710G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064914.2;CAF=[0.9789,0.02112];COMMON=1 1 8424311 rs267598736 G A . . RS=267598736;RSPOS=8424311;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=RERE:473;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8424311G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064915.2 1 8525931 rs267598738 G A . . RS=267598738;RSPOS=8525931;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=RERE:473;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8525931G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064917.2 1 8924024 rs267598749 G A . . RS=267598749;RSPOS=8924024;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=ENO1:2023;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8924024G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064928.2 1 8924025 rs267598750 G A . . RS=267598750;RSPOS=8924025;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=ENO1:2023;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.8924025G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064929.2 1 9030973 rs267598758 C T . . RS=267598758;RSPOS=9030973;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=CA6:765;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9030973C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064939.2 1 9078340 rs267598762 G A . . RS=267598762;RSPOS=9078340;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC2A7:155184;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9078340G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064943.2 1 9078399 rs267598763 C T . . RS=267598763;RSPOS=9078399;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC2A7:155184;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9078399C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064944.2 1 9097813 rs267598764 G A . . RS=267598764;RSPOS=9097813;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=SLC2A5:6518;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9097813G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064945.2 1 9305316 rs398122818 AC A . . RS=398122818;RSPOS=9305318;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110200;GENEINFO=H6PD:9563;WGT=0;VC=DIV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9305318delC;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0006;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024293.26 1 9322320 rs398122817 C G . . RS=398122817;RSPOS=9322320;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9322320C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0005;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024292.26 1 9322332 rs398122816 G A . . RS=398122816;RSPOS=9322332;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9322332G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024290.26 1 9323628 rs387907167 G A . . RS=387907167;RSPOS=9323628;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9323628G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=138090.0004;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet:SNOMED_CT;CLNDSDBID=C1291245:604931:168588:124138004;CLNDBN=Deficiency_of_(R)-20-hydroxysteroid_dehydrogenase;CLNACC=RCV000024291.26 1 9323910 rs6688832 G A . . RS=6688832;RSPOS=9323910;dbSNPBuildID=116;SSR=0;SAO=1;VP=0x05036800000015051f110101;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;PMC;S3D;SLO;VLD;G5;HD;GNO;KGPhase1;KGPilot123;KGPROD;OTHERKG;PH3;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.9323910G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=0;CLNSRCID=138090.0002;CLNSIG=0;CLNDSDB=.;CLNDSDBID=.;CLNDBN=Reclassified_-_variant_of_unknown_significance;CLNACC=RCV000017511.1;CAF=[0.6364,0.3636];COMMON=1 1 9324187 rs267598769 C T . . RS=267598769;RSPOS=9324187;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;GENEINFO=H6PD:9563;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9324187C>T;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064951.2 1 9780198 rs141809100 G A . . RS=141809100;RSPOS=9780198;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=PIK3CD:5293;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9780198G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060269.2 1 9780199 rs147135836 G A . . RS=147135836;RSPOS=9780199;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050268000000000002100120;GENEINFO=PIK3CD:5293;WGT=0;VC=SNV;PM;PMC;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9780199G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060270.2 1 9787030 rs397518423 G A . . RS=397518423;RSPOS=9787030;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060000000000002100100;GENEINFO=PIK3CD:5293;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9787030G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=602839.0001;CLNSIG=5|5;CLNDSDB=MedGen|OMIM;CLNDSDBID=CN181202|615513;CLNDBN=Activated_PI3K-Delta_Syndrome_(APDS)|ACTIVATED_PI3K-DELTA_SYNDROME;CLNACC=RCV000074362.1|RCV000076908.2 1 9804551 rs267598783 G A . . RS=267598783;RSPOS=9804551;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9804551G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064965.2 1 9804656 rs140324308 G A . . RS=140324308;RSPOS=9804656;dbSNPBuildID=134;SSR=0;SAO=3;VP=0x050068000000000002100120;WGT=0;VC=SNV;PM;PMC;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9804656G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000060271.2 1 9809643 rs267598784 G A . . RS=267598784;RSPOS=9809643;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050060000000000002100120;WGT=0;VC=SNV;PM;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.9809643G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064966.2 1 10032156 rs387907294 G A . . RS=387907294;RSPOS=10032156;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10032156G>A;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0009;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030771.1 1 10042370 rs387907292 G T . . RS=387907292;RSPOS=10042370;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042370G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0004;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030767.1 1 10042376 rs387907293 C G . . RS=387907293;RSPOS=10042376;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050060000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042376C>G;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0008;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030770.1 1 10042538 rs142968179 C T . . RS=142968179;RSPOS=10042538;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050260000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042538C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0005;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030764.1 1 10042614 rs267598792 G A . . RS=267598792;RSPOS=10042614;dbSNPBuildID=137;SSR=0;SAO=3;VP=0x050260000000000002100120;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042614G>A;CLNSRC=.;CLNORIGIN=2;CLNSRCID=.;CLNSIG=1;CLNDSDB=MedGen:SNOMED_CT;CLNDSDBID=C0025202:2092003;CLNDBN=Malignant_melanoma;CLNACC=RCV000064974.2 1 10042629 rs368062092 G T . . RS=368062092;RSPOS=10042629;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050260000000000002110100;GENEINFO=NMNAT1:64802;WGT=0;VC=SNV;PM;S3D;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.10042629G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=.;CLNSRCID=608700.0007;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1298:C1837873:608553:65;CLNDBN=Leber_congenital_amaurosis_9;CLNACC=RCV000030769.1 bio-vcf-0.9.5/test/data/input/empty.vcf000066400000000000000000000000741400124230400177260ustar00rootroot00000000000000##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO bio-vcf-0.9.5/test/data/input/gatk_exome.vcf000066400000000000000000001224441400124230400207210ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= 13.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= 200.0"> ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CONTROLP25 CONTROLP26 1 22848972 rs61769198 A C 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. 1 33133968 rs2762904 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 60466814 rs626251 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 60466840 rs35944236 TA T 18.20 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=9.10;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:53,6,0 1 62516683 rs2498982 G C 114.46 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.62;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,4:4:12:141,12,0 1 66058513 rs1137101 A G 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 95709821 rs259358 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 109806834 rs6698843 C T 46.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.08;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 ./. 1 114354942 rs3789604 T G 47.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.58;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:73,6,0 1 144873962 rs11341221 CT C 46.13 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.52;MQ0=0;QD=23.07;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 ./. 1 151733335 rs8480 T G 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 ./. 1 157516779 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 197479688 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 228005073 rs200455452 C T 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 228465370 rs867599 T G 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 1 231488524 rs2437150 C T 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:69,6,0 1 235505313 rs3841735 A AT 26.14 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=13.07;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 ./. 1 237951451 rs2256242 A G 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 2 27682309 rs61747073 C T 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 2 32667182 rs60197615 G C 40.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:66,6,0 2 37406680 rs10205833 C G 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 2 112705157 rs3761701 T C 40.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:66,6,0 2 113513825 rs6731822 T C 41.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 ./. 2 152403960 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 2 207998800 rs2284934 C T 40.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:66,6,0 3 8667896 rs355058 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 3 57368861 . CT C 32.13 PASS AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.07;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:67,6,0 3 62478014 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. 3 75787726 rs1962893 G A 20 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 ./. 3 75787739 rs141238251 A T 20 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 ./. 3 101484335 rs2625282 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 3 119434527 rs6438544 G C 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.45;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,1:1:6:70,6,0 3 119434528 . C A 44.17 PASS AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 3 121168152 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. 3 121822564 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 3 122437321 rs7645033 T C 55.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.57;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:82,9,0 3 134225969 rs9827878 T C 46.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.08;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:72,6,0 3 139244744 . T C 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 4 48037926 rs13116684 A G 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:68,6,0 4 100572396 . T C 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 5 32400266 rs1051489 A G 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:69,6,0 5 64070617 rs140062546 A AAATTATGAC 55.13 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.57;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:90,6,0 5 74442920 rs6888707 A G 46.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.08;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 ./. 5 89990324 rs1878878 A G 32.21 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=10.74;ReadPosRankSum=0.736;set=Intersection GT:AD:DP:GQ:PL 0/1:1,2:3:26:59,0,26 ./. 5 102894673 rs34468716 T C 20.21 LowQual AC=2;AF=0.500;AN=4;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=6;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=10.11;ReadPosRankSum=0.736;set=FilteredInAll GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,34 1/1:0,2:2:6:49,6,0 5 145519821 rs17493851 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 5 178139442 rs1132338 T G 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 5 178996435 rs11743261 A G 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 6 335175 rs2671431 A T 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 6 12122645 rs6900196 A G 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 6 29407970 rs2074469 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 6 29523676 rs8337 C G 47.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.58;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:73,6,0 6 47649222 rs8180544 T G 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 6 56417282 rs4715630 C T 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 6 90448092 rs4140446 C T 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:68,6,0 6 106992464 rs1799693 A G 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 6 121632008 rs9372653 T A 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:68,6,0 6 138754323 rs2327891 A G 79.84 PASS AC=4;AF=1.00;AN=4;DB;DP=6;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.61;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 1/1:0,1:1:3:35,3,0 6 159188128 rs2242318 A G 74.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.90;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:101,9,0 6 160962177 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 7 6370144 rs1043965 G A 32.21 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=10.74;ReadPosRankSum=-0.736;set=Intersection GT:AD:DP:GQ:PL ./. 0/1:1,2:3:26:59,0,26 7 12376811 rs2192828 A C 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:69,6,0 7 15584409 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 7 22202052 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 7 25266626 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 7 31617733 rs6945679 T C 91.46 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.87;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,4:4:12:118,12,0 7 42976789 rs630191 A G 58.84 PASS AC=4;AF=1.00;AN=4;DB;DP=6;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=19.61;set=Intersection GT:AD:DP:GQ:PL 1/1:0,1:1:3:35,3,0 1/1:0,2:2:6:49,6,0 7 92762681 rs1029357 A G 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 ./. 7 100551840 rs78273697 T A 64.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.08;set=filterInvariant-variant2 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:90,6,0 7 100551842 rs75365561 C T 64.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.08;set=filterInvariant-variant2 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:90,6,0 7 100551843 rs75524285 T C 100.84 PASS AC=4;AF=1.00;AN=4;DB;DP=4;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.63;set=filterInvariant-variant2 GT:AD:DP:GQ:PL 1/1:.:.:3:36,3,0 1/1:0,2:2:6:90,6,0 7 100551849 rs77242346 A T 100.84 PASS AC=4;AF=1.00;AN=4;DB;DP=6;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.61;set=filterInvariant-variant2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:36,3,0 1/1:0,2:2:6:90,6,0 7 100552644 rs2904850 C A 39.17 PASS AC=2;AF=0.500;AN=4;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=6;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=19.59;ReadPosRankSum=-0.736;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 0/0:1,0:1:3:0,3,36 7 100552788 rs73398800 C T 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 7 100552867 rs73714266 T C 44.42 PASS AC=4;AF=1.00;AN=4;DB;DP=4;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.21;set=Intersection GT:AD:DP:GQ:PL 1/1:0,1:1:3:35,3,0 1/1:0,1:1:3:34,3,0 7 142460335 rs201550522 A G 20 LowQual;MappingQuality AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:45,3,0 7 142460339 rs200973660 G A 20 LowQual;MappingQuality AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:45,3,0 7 151970856 rs10454320 T A 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=42.05;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 7 151970931 rs56850341 G A 29.18 LowQual;MappingQuality AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.12;MQ0=0;QD=14.59;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:55,6,0 ./. 7 154862621 rs6320 T A 38.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=19.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 ./. 8 29023297 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 9 390512 rs2297075 C T 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 9 21334694 . T C 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 9 79117556 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 9 86465131 rs58077086 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 9 109687403 rs17723637 A G 46.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.08;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 ./. 9 129595895 rs3118994 T C 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:69,6,0 10 30728101 rs1042058 T C 38.17 PASS AC=2;AF=0.500;AN=4;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=6;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=19.09;ReadPosRankSum=-0.736;set=Intersection GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,35 1/1:0,2:2:6:67,6,0 10 45958881 rs2291429 A G 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:71,6,0 10 70405855 rs3998860 A G 79.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.57;set=Intersection GT:AD:DP:GQ:PL 1/1:0,3:3:9:106,9,0 ./. 10 95381773 rs701865 T A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 10 105762591 rs805657 G A 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 ./. 10 116013432 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 10 126691605 rs201760950 C A 20 LowQual;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:45,3,0 10 126691608 rs200173220 C T 20 LowQual;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:45,3,0 10 126691631 rs3198936 T A 20 LowQual;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:45,3,0 10 126691634 rs75794788 T A 20 LowQual;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=20.00;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:45,3,0 11 2929552 rs429886 A G 46.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.08;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:72,6,0 11 11373635 rs1056963 C T 40.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.60;MQ0=0;QD=20.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:66,6,0 11 55872657 rs28681529 A C 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.50;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:71,6,0 11 63883985 rs614397 T C 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 11 63885632 rs4379854 A G 56.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.90;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:83,9,0 11 74676794 rs514534 G C 59.84 PASS AC=4;AF=1.00;AN=4;DB;DP=6;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=19.95;set=Intersection GT:AD:DP:GQ:PL 1/1:0,1:1:3:36,3,0 1/1:0,2:2:6:49,6,0 11 112041128 rs45579043 TTTTGTCCTG T 55.13 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.57;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:90,6,0 11 124266912 rs28398895 A G 46.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.08;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:72,6,0 11 130064131 . G A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 12 2788879 rs1051375 G A 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. 12 10588581 rs28403159 T C 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 12 11214360 rs73260771 C T 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 ./. 12 22646247 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 12 30823971 rs1054426 A G 41.17 PASS AC=2;AF=0.500;AN=4;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=6;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=20.59;ReadPosRankSum=0.736;set=Intersection GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,35 1/1:0,2:2:6:70,6,0 12 53722128 rs7139272 G A 40.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 ./. 12 55820121 rs6581046 C T 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 12 80889165 rs145970310 T TTTG 55.13 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.57;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 ./. 12 82792942 rs10506873 A G 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 12 96653501 rs4762144 C T 56.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.90;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:83,9,0 12 123067501 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 13 32913055 rs206075 A G 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 ./. 13 46170719 rs142875900 CCCAGATACTCTTCCTCCT C 55.13 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=27.57;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 ./. 13 103514737 rs201185418 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 13 107145463 rs7995379 G C 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:71,6,0 14 21469151 rs2234636 T C 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 14 21831112 rs10146717 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 14 45623122 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 14 57101682 rs913742 A G 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:71,6,0 14 70515779 rs61977411 G A 55.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.57;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:82,9,0 14 81610583 rs1991517 G C 59.84 PASS AC=4;AF=1.00;AN=4;DB;DP=6;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=19.95;set=Intersection GT:AD:DP:GQ:PL 1/1:0,1:1:3:36,3,0 1/1:0,2:2:6:49,6,0 14 88651962 rs17762463 C T 41.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:67,6,0 14 105407798 rs4465542 T C 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 ./. 15 22368862 rs1835183 G A 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. 15 44184197 rs112105930 C T 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:69,6,0 15 65903398 rs4366668 G A 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:68,6,0 15 69728949 rs3825858 A G 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. 16 3646215 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 16 11001770 rs34654419 G T 56.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.90;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:83,9,0 16 14340388 . C A 20.21 LowQual AC=2;AF=0.500;AN=4;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=6;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=10.11;ReadPosRankSum=0.736;set=FilteredInAll GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,37 1/1:0,2:2:6:49,6,0 16 56436917 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 16 82033612 rs16956174 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 16 88712511 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 17 3632836 rs1716 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 17 8363486 . C A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. 17 9515777 rs6503235 G A 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:68,6,0 18 31324934 rs7232237 A G 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 ./. 18 56203447 rs3809979 A G 83.84 PASS AC=4;AF=1.00;AN=4;DB;DP=6;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.95;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 1/1:0,1:1:3:37,3,0 19 3434413 rs2302220 C G 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 19 6413578 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 19 11221454 rs2738442 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 19 21492062 rs547516 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.14;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 19 22952111 rs34726149 A G 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. 19 33444511 rs80283382 T C 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 ./. 19 38378539 rs10422056 G C 41.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:67,6,0 19 39915637 rs31727 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 19 48389425 rs11083907 A G 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:69,6,0 19 53085659 rs366793 C T 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 19 53344051 rs112227284 T C 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 19 53912242 rs10426347 G A 76.71 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.57;set=Intersection GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0 ./. 19 55597421 . A G 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 19 57931553 rs10417533 C T 20.21 LowQual AC=2;AF=0.500;AN=4;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=6;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=10.11;ReadPosRankSum=0.736;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 0/0:1,0:1:3:0,3,33 20 1356261 rs6074549 G C 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 ./. 20 29625877 rs7266938 G A 34.17 PASS AC=2;AF=0.500;AN=4;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=6;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=46.65;MQ0=0;MQRankSum=-0.736;QD=17.09;ReadPosRankSum=0.736;set=Intersection GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,33 1/1:0,2:2:6:63,6,0 20 29628431 rs11152458 C T 42.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.80;MQ0=0;QD=21.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:68,6,0 20 44839078 . A T 44.17 PASS AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:70,6,0 21 46957794 rs1051266 T C 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 21 47786817 rs2839228 C G 47.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.58;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:73,6,0 22 22550510 rs2073448 T G 45.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.59;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:71,6,0 22 22569448 rs5750741 T A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. 22 30771554 rs2015035 T G 46.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.08;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 ./. 22 36587845 rs5845253 A ACT 55.13 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.57;set=Intersection GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:90,6,0 22 40800544 rs2235318 C T 44.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. 22 41075543 rs133072 A G 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. 22 43936213 . G A 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 22 43936228 . G T 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 X 55172537 rs1047054 G A 43.17 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.59;set=Intersection GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. X 107911706 . T C 23.19 LowQual AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:49,6,0 X 134713855 rs2298301 G A 23.19 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.60;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. bio-vcf-0.9.5/test/data/input/gatk_wgs.vcf000066400000000000000000010547411400124230400204110ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER== 4 && ((MQ0 / (1.0 * DP)) > 0.1)"> ##FILTER= ##FILTER= ##FILTER= 30.0 && QUAL < 50.0 "> ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##GATKCommandLine== 4 && ((MQ0 / (1.0 * DP)) > 0.1), QUAL < 30.0 , QUAL > 30.0 && QUAL < 50.0 , QD < 1.5 ] filterName=[HARD_TO_VALIDATE, VeryLowQual, LowQual, LowQD] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BOXTELBLOOD0072 STE007212 STE007223 STE007231 1 10291 . C T 169.20 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.946;DP=905;Dels=0.00;FS=4.440;HaplotypeScore=72.3757;MLEAC=3;MLEAF=0.375;MQ=20.83;MQ0=368;MQRankSum=-0.438;QD=0.25;ReadPosRankSum=-3.435 GT:AD:DP:GQ:PL 0/0:219,12:238:19:0,19,348 0/1:202,24:226:99:111,0,453 0/1:189,19:213:13:13,0,419 0/1:192,30:225:79:79,0,172 1 10303 . C T 89.99 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.160;DP=980;Dels=0.00;FS=11.007;HaplotypeScore=93.8187;MLEAC=3;MLEAF=0.375;MQ=20.36;MQ0=417;MQRankSum=0.361;QD=0.12;ReadPosRankSum=2.586 GT:AD:DP:GQ:PL 0/0:231,12:250:53:0,53,640 0/1:218,26:245:53:53,0,444 0/1:209,23:234:54:54,0,421 0/1:221,24:247:17:17,0,267 1 10309 . C T 82.17 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.075;DP=975;Dels=0.00;FS=1.641;HaplotypeScore=93.7235;MLEAC=3;MLEAF=0.375;MQ=20.10;MQ0=426;MQRankSum=-0.585;QD=0.11;ReadPosRankSum=0.507 GT:AD:DP:GQ:PL 0/0:223,20:248:42:0,42,404 0/1:222,23:247:12:12,0,543 0/1:207,21:231:56:56,0,369 0/1:219,27:248:48:48,0,208 1 10321 . C T 97.17 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.176;DP=974;Dels=0.01;FS=1.382;HaplotypeScore=138.5280;MLEAC=3;MLEAF=0.375;MQ=19.93;MQ0=431;MQRankSum=-1.181;QD=0.13;ReadPosRankSum=0.841 GT:AD:DP:GQ:PL 0/0:232,14:248:27:0,27,454 0/1:222,24:247:17:17,0,517 0/1:203,22:226:14:14,0,536 0/1:206,32:241:99:100,0,352 1 10327 . T C 410.69 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.510;DP=971;Dels=0.03;FS=0.000;HaplotypeScore=162.8983;MLEAC=3;MLEAF=0.375;MQ=19.64;MQ0=442;MQRankSum=1.174;QD=0.56;ReadPosRankSum=2.600 GT:AD:DP:GQ:PL 0/1:170,59:233:99:191,0,217 0/1:159,71:232:28:28,0,528 0/0:155,68:225:5:0,5,548 0/1:166,67:234:99:224,0,352 1 10583 . G A 104.97 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-4.066;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.2479;MLEAC=4;MLEAF=0.500;MQ=38.29;MQ0=0;MQRankSum=-0.025;QD=1.61;ReadPosRankSum=-0.262 GT:AD:DP:GQ:PL 0/1:17,3:20:22:22,0,349 0/1:15,3:18:38:38,0,412 0/1:10,4:14:51:51,0,213 0/1:11,2:13:26:26,0,271 1 10694 . C G 31.59 HARD_TO_VALIDATE;LowQual AC=4;AF=1.00;AN=4;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=19.63;MQ0=4;QD=7.90 GT:AD:DP:GQ:PL 1/1:0,2:2:3:33,3,0 1/1:0,2:2:3:22,3,0 ./. ./. 1 12783 . G A 2537.43 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=6.111;DP=360;Dels=0.00;FS=0.000;HaplotypeScore=1.4766;MLEAC=5;MLEAF=0.625;MQ=14.40;MQ0=231;MQRankSum=-2.807;QD=7.05;ReadPosRankSum=-0.956 GT:AD:DP:GQ:PL 0/1:18,79:97:48:677,0,48 1/1:22,69:91:11:626,11,0 0/1:17,56:74:33:575,0,33 0/1:20,77:97:42:693,0,42 1 13110 . G A 146.12 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.768;DP=235;Dels=0.00;FS=7.537;HaplotypeScore=7.8627;MLEAC=3;MLEAF=0.375;MQ=23.13;MQ0=62;MQRankSum=-3.525;QD=0.84;ReadPosRankSum=1.463 GT:AD:DP:GQ:PL 0/1:54,5:59:1:1,0,884 0/1:53,13:66:95:95,0,911 0/1:39,9:48:78:78,0,740 0/0:54,8:62:0:0,0,911 1 13116 . T G 1695.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.956;DP=205;Dels=0.00;FS=109.365;HaplotypeScore=6.7694;MLEAC=4;MLEAF=0.500;MQ=22.66;MQ0=60;MQRankSum=-8.991;QD=8.27;ReadPosRankSum=-0.018 GT:AD:DP:GQ:PL 0/1:19,28:47:99:337,0,294 0/1:19,43:62:99:632,0,259 0/1:22,24:46:99:288,0,425 0/1:15,35:50:99:471,0,283 1 13118 . A G 1589.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-3.916;DP=197;Dels=0.00;FS=98.775;HaplotypeScore=6.2308;MLEAC=4;MLEAF=0.500;MQ=22.10;MQ0=60;MQRankSum=-8.206;QD=8.07;ReadPosRankSum=-0.222 GT:AD:DP:GQ:PL 0/1:18,27:45:99:340,0,276 0/1:18,38:56:99:552,0,245 0/1:21,23:44:99:263,0,405 0/1:15,36:51:99:467,0,285 1 13302 . C T 458.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=4.082;DP=189;Dels=0.00;FS=30.039;HaplotypeScore=1.0973;MLEAC=4;MLEAF=0.500;MQ=23.65;MQ0=79;MQRankSum=-8.041;QD=2.43;ReadPosRankSum=-4.139 GT:AD:DP:GQ:PL 0/1:22,31:53:99:118,0,498 0/1:19,25:44:99:161,0,400 0/1:24,18:42:32:32,0,514 0/1:20,28:48:99:180,0,337 1 13649 . G C 93.17 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.681;DP=224;Dels=0.00;FS=0.000;HaplotypeScore=22.7737;MLEAC=2;MLEAF=0.250;MQ=14.02;MQ0=124;MQRankSum=0.981;QD=0.80;ReadPosRankSum=1.571 GT:AD:DP:GQ:PL 0/1:60,9:69:58:58,0,549 0/1:41,7:48:69:69,0,232 0/0:47,5:53:51:0,51,490 0/0:50,4:54:12:0,12,335 1 13878 . G C 79.98 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.476;DP=412;Dels=0.00;FS=11.677;HaplotypeScore=0.9186;MLEAC=2;MLEAF=0.250;MQ=12.15;MQ0=266;MQRankSum=2.129;QD=0.39;ReadPosRankSum=0.958 GT:AD:DP:GQ:PL 0/0:81,14:95:55:0,55,707 0/1:93,11:104:20:20,0,438 0/1:89,13:102:94:94,0,432 0/0:104,7:111:55:0,55,722 1 14354 . C A 31.58 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=1.468;DP=285;Dels=0.00;FS=7.782;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=4.82;MQ0=273;MQRankSum=0.600;QD=0.16;ReadPosRankSum=-0.289 GT:AD:DP:GQ:PL 0/0:75,14:89:3:0,3,30 0/1:56,12:68:18:18,0,71 0/1:51,13:64:21:21,0,48 0/1:51,13:64:22:24,0,22 1 14522 . G A 68.10 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=3.152;DP=209;Dels=0.00;FS=14.099;HaplotypeScore=1.3722;MLEAC=3;MLEAF=0.375;MQ=14.74;MQ0=136;MQRankSum=-0.235;QD=0.42;ReadPosRankSum=4.774 GT:AD:DP:GQ:PL 0/0:40,6:46:18:0,18,202 0/1:48,12:60:17:17,0,283 0/1:37,8:45:32:32,0,172 0/1:47,11:58:53:53,0,410 1 14542 . A G 54.12 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.506;DP=229;Dels=0.00;FS=2.344;HaplotypeScore=0.5390;MLEAC=3;MLEAF=0.375;MQ=13.76;MQ0=148;MQRankSum=-0.456;QD=0.30;ReadPosRankSum=2.092 GT:AD:DP:GQ:PL 0/0:44,6:50:27:0,27,305 0/1:57,12:69:5:5,0,416 0/1:40,8:48:26:26,0,236 0/1:51,11:62:56:56,0,390 1 14673 . G C 340.98 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.410;DP=200;Dels=0.00;FS=54.600;HaplotypeScore=3.8518;MLEAC=4;MLEAF=0.500;MQ=21.00;MQ0=79;MQRankSum=0.098;QD=1.70;ReadPosRankSum=1.165 GT:AD:DP:GQ:PL 0/1:38,18:56:99:225,0,426 0/1:34,14:48:99:104,0,506 0/1:29,12:41:24:24,0,496 0/1:41,14:55:20:20,0,549 1 14699 . C G 436.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=6.043;DP=214;Dels=0.00;FS=20.309;HaplotypeScore=1.8510;MLEAC=4;MLEAF=0.500;MQ=22.16;MQ0=63;MQRankSum=-2.196;QD=2.04;ReadPosRankSum=-0.814 GT:AD:DP:GQ:PL 0/1:33,21:54:99:128,0,337 0/1:37,12:49:36:36,0,585 0/1:34,11:45:83:83,0,678 0/1:40,26:66:99:222,0,562 1 14907 . A G 4600.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.701;DP=322;Dels=0.00;FS=16.855;HaplotypeScore=2.9484;MLEAC=4;MLEAF=0.500;MQ=31.50;MQ0=22;MQRankSum=1.772;QD=14.29;ReadPosRankSum=0.119 GT:AD:DP:GQ:PL 0/1:38,53:91:99:1082,0,502 0/1:30,56:86:99:1394,0,463 0/1:19,45:64:99:1016,0,333 0/1:32,49:81:99:1141,0,593 1 14930 . A G 4086.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-7.443;DP=320;Dels=0.00;FS=4.792;HaplotypeScore=3.2020;MLEAC=4;MLEAF=0.500;MQ=33.77;MQ0=7;MQRankSum=0.194;QD=12.77;ReadPosRankSum=1.052 GT:AD:DP:GQ:PL 0/1:32,52:84:99:895,0,580 0/1:26,53:79:99:1135,0,468 0/1:22,47:69:99:934,0,521 0/1:30,58:88:99:1155,0,610 1 15015 . G C 256.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.245;DP=287;Dels=0.00;FS=77.878;HaplotypeScore=2.4024;MLEAC=3;MLEAF=0.375;MQ=19.83;MQ0=138;MQRankSum=-1.053;QD=1.19;ReadPosRankSum=5.830 GT:AD:DP:GQ:PL 0/0:66,6:72:63:0,63,651 0/1:64,10:74:90:90,0,720 0/1:53,9:62:99:109,0,568 0/1:64,15:79:92:92,0,797 1 15045 . C T 214.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=3.992;DP=269;Dels=0.00;FS=44.451;HaplotypeScore=0.9104;MLEAC=3;MLEAF=0.375;MQ=15.66;MQ0=145;MQRankSum=3.074;QD=1.04;ReadPosRankSum=0.394 GT:AD:DP:GQ:PL 0/0:58,5:63:54:0,54,505 0/1:64,10:74:94:94,0,674 0/1:50,7:57:64:64,0,489 0/1:61,14:75:91:91,0,491 1 15118 . A G 1625.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.642;DP=304;Dels=0.00;FS=5.636;HaplotypeScore=2.0188;MLEAC=4;MLEAF=0.500;MQ=21.05;MQ0=78;MQRankSum=-0.305;QD=5.35;ReadPosRankSum=-1.493 GT:AD:DP:GQ:PL 0/1:48,23:71:99:406,0,670 0/1:54,24:80:99:461,0,725 0/1:47,28:76:99:464,0,635 0/1:52,25:77:99:327,0,877 1 15190 . G A 655.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=4.541;DP=326;Dels=0.00;FS=14.928;HaplotypeScore=2.2227;MLEAC=4;MLEAF=0.500;MQ=25.88;MQ0=64;MQRankSum=-2.193;QD=2.01;ReadPosRankSum=-0.217 GT:AD:DP:GQ:PL 0/1:71,18:90:99:205,0,1221 0/1:71,15:86:99:165,0,1245 0/1:58,15:73:99:166,0,1069 0/1:59,17:77:99:152,0,1268 1 15211 . T G 4577.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-6.741;DP=304;Dels=0.00;FS=0.000;HaplotypeScore=2.0978;MLEAC=4;MLEAF=0.500;MQ=26.85;MQ0=55;MQRankSum=0.371;QD=15.06;ReadPosRankSum=-2.341 GT:AD:DP:GQ:PL 0/1:25,54:79:99:1074,0,197 0/1:16,67:83:99:1342,0,113 0/1:14,50:64:99:948,0,184 0/1:23,55:78:99:1246,0,221 1 15274 . A T 2908.09 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.557;DP=204;Dels=0.00;FS=0.000;HaplotypeScore=3.0034;MLEAC=7;MLEAF=0.875;MQ=22.35;MQ0=66;MQRankSum=0.975;QD=14.26;ReadPosRankSum=0.044 GT:AD:DP:GQ:PL 1/1:0,37:53:81:800,81,0 1/1:0,37:44:75:739,75,0 1/1:0,29:46:69:702,69,0 1/1:1,45:60:74:950,74,0 1 15484 . G A 152.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.783;DP=293;Dels=0.00;FS=9.762;HaplotypeScore=2.0763;MLEAC=3;MLEAF=0.375;MQ=17.27;MQ0=132;MQRankSum=-0.308;QD=0.72;ReadPosRankSum=-0.964 GT:AD:DP:GQ:PL 0/0:75,6:81:87:0,87,844 0/1:65,14:79:68:68,0,905 0/1:48,13:61:67:67,0,525 0/1:61,10:71:52:52,0,737 1 16014 . C T 305.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.480;DP=109;Dels=0.00;FS=46.948;HaplotypeScore=1.5285;MLEAC=4;MLEAF=0.500;MQ=12.96;MQ0=73;MQRankSum=2.235;QD=2.81;ReadPosRankSum=-0.844 GT:AD:DP:GQ:PL 0/1:18,8:26:70:70,0,86 0/1:20,14:34:32:128,0,32 0/1:19,4:23:39:39,0,64 0/1:17,9:26:35:101,0,35 1 16068 . T C 682.66 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=-1.733;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=21.18;MQ0=22;MQRankSum=1.631;QD=12.19;ReadPosRankSum=1.019 GT:AD:DP:GQ:PL 1/1:0,9:9:6:53,6,0 1/1:2,22:24:30:282,30,0 1/1:0,9:9:15:139,15,0 1/1:0,13:14:27:234,27,0 1 16103 . T G 1654.37 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.229;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=24.23;MQ0=34;MQRankSum=1.509;QD=17.23;ReadPosRankSum=-1.285 GT:AD:DP:GQ:PL 1/1:0,16:17:18:201,18,0 1/1:1,38:39:60:617,60,0 1/1:0,19:19:45:472,45,0 1/1:0,21:21:39:390,39,0 1 16257 . G C 1123.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.178;DP=230;Dels=0.00;FS=0.871;HaplotypeScore=2.6943;MLEAC=4;MLEAF=0.500;MQ=27.52;MQ0=50;MQRankSum=1.621;QD=4.89;ReadPosRankSum=0.056 GT:AD:DP:GQ:PL 0/1:46,22:68:99:370,0,794 0/1:31,25:56:99:359,0,605 0/1:37,15:52:99:224,0,663 0/1:40,14:54:99:203,0,799 1 16288 . C G 196.15 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.029;DP=109;Dels=0.00;FS=8.923;HaplotypeScore=1.4846;MLEAC=4;MLEAF=0.500;MQ=21.92;MQ0=35;MQRankSum=-1.274;QD=1.80;ReadPosRankSum=-0.124 GT:AD:DP:GQ:PL 0/1:23,6:29:59:59,0,393 0/1:20,7:27:96:96,0,286 0/1:21,7:28:62:62,0,293 0/1:20,5:25:11:11,0,296 1 16298 . C T 910.39 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.4419;MLEAC=8;MLEAF=1.00;MQ=16.62;MQ0=33;QD=11.52 GT:AD:DP:GQ:PL 1/1:0,18:18:30:273,30,0 1/1:0,21:22:27:249,27,0 1/1:0,18:18:15:142,15,0 1/1:0,21:21:30:272,30,0 1 16378 . T C 3043.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-6.537;DP=389;Dels=0.00;FS=5.431;HaplotypeScore=1.2797;MLEAC=4;MLEAF=0.500;MQ=17.53;MQ0=197;MQRankSum=-0.836;QD=7.83;ReadPosRankSum=-0.421 GT:AD:DP:GQ:PL 0/1:32,67:99:73:811,0,73 0/1:36,77:113:99:838,0,171 0/1:27,57:85:32:799,0,32 0/1:30,62:92:63:628,0,63 1 16495 . G C 1966.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-9.239;DP=288;Dels=0.00;FS=0.618;HaplotypeScore=10.2366;MLEAC=4;MLEAF=0.500;MQ=26.82;MQ0=47;MQRankSum=-0.369;QD=6.83;ReadPosRankSum=-1.074 GT:AD:DP:GQ:PL 0/1:39,30:69:99:583,0,519 0/1:50,30:80:99:446,0,734 0/1:46,33:79:99:553,0,871 0/1:34,26:60:99:417,0,689 1 16497 . A G 149.01 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.196;DP=282;Dels=0.00;FS=0.000;HaplotypeScore=10.1968;MLEAC=3;MLEAF=0.375;MQ=26.81;MQ0=49;MQRankSum=-3.719;QD=0.69;ReadPosRankSum=-1.428 GT:AD:DP:GQ:PL 0/0:57,8:66:99:0,119,1395 0/1:64,13:77:16:16,0,1187 0/1:63,18:81:99:108,0,1423 0/1:48,10:58:59:59,0,1121 1 16534 . C T 1650.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.115;DP=210;Dels=0.00;FS=2.044;HaplotypeScore=1.1672;MLEAC=4;MLEAF=0.500;MQ=21.39;MQ0=68;MQRankSum=2.751;QD=7.86;ReadPosRankSum=-1.971 GT:AD:DP:GQ:PL 0/1:15,28:43:99:338,0,193 0/1:42,29:71:99:400,0,439 0/1:21,30:51:99:499,0,255 0/1:21,24:45:99:446,0,216 1 16571 . G A 876.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.268;DP=172;Dels=0.00;FS=11.474;HaplotypeScore=3.9389;MLEAC=4;MLEAF=0.500;MQ=14.19;MQ0=97;MQRankSum=2.204;QD=5.10;ReadPosRankSum=0.507 GT:AD:DP:GQ:PL 0/1:21,26:47:68:237,0,68 0/1:26,24:50:99:311,0,176 0/1:16,15:31:99:200,0,141 0/1:29,15:44:74:161,0,74 1 16580 . C G 145.70 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.744;DP=175;Dels=0.00;FS=4.663;HaplotypeScore=3.9389;MLEAC=3;MLEAF=0.375;MQ=13.85;MQ0=104;MQRankSum=-0.051;QD=1.15;ReadPosRankSum=2.218 GT:AD:DP:GQ:PL 0/1:41,7:48:98:98,0,210 0/1:44,7:51:41:41,0,427 0/1:24,4:28:40:40,0,255 0/0:44,4:48:9:0,9,277 1 16631 . T C 44.13 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-3.754;DP=204;Dels=0.00;FS=0.000;HaplotypeScore=0.7033;MLEAC=2;MLEAF=0.250;MQ=13.58;MQ0=127;MQRankSum=-1.439;QD=0.36;ReadPosRankSum=-0.810 GT:AD:DP:GQ:PL 0/1:60,5:65:52:52,0,572 0/1:53,4:57:26:26,0,362 0/0:26,0:26:18:0,18,166 0/0:50,4:54:15:0,15,336 1 16841 . G T 210.13 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.139;DP=194;Dels=0.00;FS=0.000;HaplotypeScore=2.6289;MLEAC=4;MLEAF=0.500;MQ=18.63;MQ0=66;MQRankSum=0.050;QD=1.08;ReadPosRankSum=0.360 GT:AD:DP:GQ:PL 0/1:40,9:49:94:94,0,478 0/1:50,4:54:3:3,0,810 0/1:27,11:38:99:101,0,426 0/1:45,5:50:43:43,0,662 1 16977 . G A 94.08 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.369;DP=366;Dels=0.00;FS=2.642;HaplotypeScore=0.6197;MLEAC=3;MLEAF=0.375;MQ=10.14;MQ0=286;MQRankSum=0.665;QD=0.35;ReadPosRankSum=1.565 GT:AD:DP:GQ:PL 0/0:73,21:94:16:0,16,370 0/1:79,30:109:30:30,0,385 0/1:62,21:83:60:60,0,261 0/1:57,23:80:38:38,0,317 1 17020 . G A 303.73 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.389;DP=375;Dels=0.00;FS=0.848;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=11.92;MQ0=265;MQRankSum=-0.936;QD=0.81;ReadPosRankSum=1.462 GT:AD:DP:GQ:PL 0/1:86,15:102:60:60,0,515 0/1:83,20:103:90:90,0,431 0/1:72,12:84:5:5,0,367 0/1:74,12:86:99:180,0,374 1 17385 . G A 890.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.169;DP=503;Dels=0.00;FS=36.376;HaplotypeScore=5.4092;MLEAC=4;MLEAF=0.500;MQ=14.80;MQ0=324;MQRankSum=3.897;QD=1.77;ReadPosRankSum=-0.810 GT:AD:DP:GQ:PL 0/1:97,22:119:99:105,0,256 0/1:98,32:130:99:297,0,646 0/1:91,30:121:99:370,0,604 0/1:107,25:132:99:151,0,720 1 17538 . C A 880.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.382;DP=312;Dels=0.00;FS=0.000;HaplotypeScore=2.4657;MLEAC=4;MLEAF=0.500;MQ=29.94;MQ0=125;MQRankSum=-0.804;QD=2.82;ReadPosRankSum=-0.094 GT:AD:DP:GQ:PL 0/1:82,12:94:99:237,0,796 0/1:67,19:86:99:400,0,840 0/1:62,13:75:99:179,0,995 0/1:48,9:57:97:97,0,608 1 17746 . A G 590.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-5.079;DP=271;Dels=0.00;FS=0.000;HaplotypeScore=1.7719;MLEAC=4;MLEAF=0.500;MQ=24.30;MQ0=138;MQRankSum=0.374;QD=2.18;ReadPosRankSum=0.811 GT:AD:DP:GQ:PL 0/1:41,15:57:86:86,0,396 0/1:61,21:82:99:212,0,772 0/1:50,21:71:99:127,0,800 0/1:37,22:59:99:198,0,339 1 19004 . A G 151.99 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-4.201;DP=193;Dels=0.00;FS=0.000;HaplotypeScore=0.1446;MLEAC=4;MLEAF=0.500;MQ=7.89;MQ0=165;MQRankSum=-0.487;QD=0.79;ReadPosRankSum=-0.580 GT:AD:DP:GQ:PL 0/1:28,24:52:52:52,0,108 0/1:19,33:53:18:42,0,18 0/1:30,16:46:58:58,0,62 0/1:20,22:42:32:32,0,112 1 19322 . C T 106.70 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.834;DP=211;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=6.75;MQ0=186;MQRankSum=-0.465;QD=0.69;ReadPosRankSum=-0.794 GT:AD:DP:GQ:PL 0/0:53,4:57:9:0,9,79 0/1:54,4:59:41:41,0,44 0/1:42,9:51:54:62,0,54 0/1:39,5:44:37:37,0,90 1 19355 . G A 73.46 HARD_TO_VALIDATE;LowQD AC=3;AF=0.500;AN=6;BaseQRankSum=1.635;DP=242;Dels=0.00;FS=0.000;HaplotypeScore=0.2217;MLEAC=3;MLEAF=0.500;MQ=4.79;MQ0=230;MQRankSum=1.000;QD=0.37;ReadPosRankSum=0.529 GT:AD:DP:GQ:PL ./. 0/1:70,12:82:36:36,0,89 0/1:50,4:54:21:22,0,21 0/1:50,13:63:18:45,0,18 1 19391 . G A 73.55 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.267;DP=220;Dels=0.00;FS=0.000;HaplotypeScore=0.8725;MLEAC=3;MLEAF=0.375;MQ=5.33;MQ0=206;MQRankSum=1.467;QD=0.44;ReadPosRankSum=0.667 GT:AD:DP:GQ:PL 0/1:39,4:44:21:21,0,21 0/1:60,10:70:39:39,0,65 0/0:48,3:51:3:0,3,26 0/1:45,10:55:18:45,0,18 1 19858 . C T 3188.97 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.384;DP=333;Dels=0.00;FS=0.000;HaplotypeScore=1.0028;MLEAC=4;MLEAF=0.500;MQ=19.98;MQ0=151;MQRankSum=0.762;QD=9.58;ReadPosRankSum=0.238 GT:AD:DP:GQ:PL 0/1:25,49:74:99:621,0,100 0/1:26,53:79:99:750,0,280 0/1:26,65:91:99:960,0,169 0/1:32,57:89:99:890,0,310 1 19942 . G C 1077.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=11.081;DP=402;Dels=0.00;FS=0.000;HaplotypeScore=12.7813;MLEAC=4;MLEAF=0.500;MQ=22.81;MQ0=127;MQRankSum=0.156;QD=2.68;ReadPosRankSum=0.543 GT:AD:DP:GQ:PL 0/1:85,26:111:99:288,0,1205 0/1:79,22:102:99:230,0,808 0/1:72,16:88:99:188,0,1097 0/1:77,24:101:99:404,0,1133 1 19952 . G T 268.13 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.052;DP=382;Dels=0.00;FS=0.000;HaplotypeScore=13.1417;MLEAC=4;MLEAF=0.500;MQ=22.45;MQ0=123;MQRankSum=-0.189;QD=0.70;ReadPosRankSum=-0.317 GT:AD:DP:GQ:PL 0/1:87,18:105:99:159,0,1313 0/1:90,11:101:80:80,0,1106 0/1:72,7:79:3:3,0,1338 0/1:82,13:95:57:57,0,1585 1 20129 . C T 1862.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=5.510;DP=546;Dels=0.00;FS=3.287;HaplotypeScore=10.8088;MLEAC=4;MLEAF=0.500;MQ=22.86;MQ0=48;MQRankSum=0.737;QD=3.41;ReadPosRankSum=-1.548 GT:AD:DP:GQ:PL 0/1:109,33:142:99:333,0,2140 0/1:82,40:122:99:666,0,1409 0/1:93,27:120:99:376,0,1823 0/1:124,37:162:99:520,0,2576 1 20144 . G A 3261.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.441;DP=596;Dels=0.00;FS=1.102;HaplotypeScore=11.1173;MLEAC=4;MLEAF=0.500;MQ=24.01;MQ0=51;MQRankSum=2.172;QD=5.47;ReadPosRankSum=-0.792 GT:AD:DP:GQ:PL 0/1:94,52:147:99:876,0,1732 0/1:106,38:144:99:561,0,2015 0/1:86,42:128:99:759,0,1823 0/1:119,58:177:99:1098,0,2380 1 20206 . C T 123.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=6.887;DP=693;Dels=0.00;FS=1.259;HaplotypeScore=23.0271;MLEAC=2;MLEAF=0.250;MQ=25.48;MQ0=150;MQRankSum=2.373;QD=0.34;ReadPosRankSum=1.063 GT:AD:DP:GQ:PL 0/0:139,15:155:99:0,139,2522 0/1:171,19:190:45:45,0,2806 0/1:154,19:173:99:113,0,2789 0/0:162,13:175:96:0,96,2839 1 20245 . G A 930.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.717;DP=627;Dels=0.00;FS=13.851;HaplotypeScore=15.5971;MLEAC=4;MLEAF=0.500;MQ=23.78;MQ0=218;MQRankSum=1.625;QD=1.48;ReadPosRankSum=1.326 GT:AD:DP:GQ:PL 0/1:119,28:147:99:181,0,1629 0/1:127,33:160:99:232,0,2139 0/1:131,28:159:99:434,0,2164 0/1:138,21:161:99:116,0,2107 1 20304 . G C 1182.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.386;DP=429;Dels=0.00;FS=16.345;HaplotypeScore=3.1384;MLEAC=4;MLEAF=0.500;MQ=14.90;MQ0=294;MQRankSum=0.725;QD=2.76;ReadPosRankSum=-1.136 GT:AD:DP:GQ:PL 0/1:68,39:107:99:333,0,314 0/1:59,51:110:99:354,0,336 0/1:56,32:89:99:300,0,443 0/1:73,49:122:99:228,0,418 1 20321 . A C 1745.48 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=1.318;DP=432;Dels=0.00;FS=9.367;HaplotypeScore=1.8208;MLEAC=4;MLEAF=0.500;MQ=10.62;MQ0=331;MQRankSum=-0.856;QD=4.04;ReadPosRankSum=-1.850 GT:AD:DP:GQ:PL 1/1:41,71:112:1:575,1,0 0/1:49,62:111:99:393,0,120 0/1:33,51:84:68:410,0,68 0/1:51,73:124:23:398,0,23 1 20467 . C T 2196.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-3.972;DP=507;Dels=0.00;FS=0.000;HaplotypeScore=2.2732;MLEAC=4;MLEAF=0.500;MQ=15.67;MQ0=306;MQRankSum=1.851;QD=4.33;ReadPosRankSum=-0.325 GT:AD:DP:GQ:PL 0/1:63,50:114:99:519,0,389 0/1:72,62:134:99:622,0,308 0/1:53,64:117:99:531,0,291 0/1:82,60:142:99:557,0,585 1 20512 . G T 1564.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.373;DP=548;Dels=0.00;FS=0.000;HaplotypeScore=0.4002;MLEAC=4;MLEAF=0.500;MQ=14.26;MQ0=401;MQRankSum=1.320;QD=2.86;ReadPosRankSum=2.050 GT:AD:DP:GQ:PL 0/1:61,50:111:99:204,0,103 0/1:90,66:157:99:520,0,465 0/1:67,62:129:99:458,0,346 0/1:83,68:151:99:415,0,431 1 20595 . A G 278.46 HARD_TO_VALIDATE;LowQD AC=5;AF=0.625;AN=8;BaseQRankSum=0.000;DP=541;Dels=0.00;FS=0.000;HaplotypeScore=1.3358;MLEAC=5;MLEAF=0.625;MQ=10.60;MQ0=493;MQRankSum=1.508;QD=0.51;ReadPosRankSum=-0.441 GT:AD:DP:GQ:PL 1/1:94,22:116:3:35,3,0 0/1:111,29:140:43:43,0,482 0/1:92,30:122:99:118,0,308 0/1:119,44:163:62:114,0,62 1 28511 . G A 64.64 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.038;DP=169;Dels=0.00;FS=0.000;HaplotypeScore=0.6569;MLEAC=3;MLEAF=0.375;MQ=5.49;MQ0=146;MQRankSum=0.635;QD=0.78;ReadPosRankSum=0.635 GT:AD:DP:GQ:PL 0/1:37,6:43:16:44,0,16 1/1:36,4:40:6:54,6,0 0/0:38,2:40:6:0,6,49 0/0:45,1:46:3:0,3,25 1 28558 . C T 63.93 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.446;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=0.8418;MLEAC=3;MLEAF=0.375;MQ=8.05;MQ0=86;MQRankSum=0.348;QD=1.07;ReadPosRankSum=1.592 GT:AD:DP:GQ:PL 0/1:19,8:27:19:44,0,19 1/1:24,9:33:6:54,6,0 0/0:28,4:32:9:0,9,76 0/0:27,6:33:3:0,3,25 1 28563 . A G 184.82 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.403;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=0.9864;MLEAC=8;MLEAF=1.00;MQ=8.32;MQ0=80;MQRankSum=-1.733;QD=1.51;ReadPosRankSum=-0.825 GT:AD:DP:GQ:PL 1/1:7,20:27:9:81,9,0 1/1:7,24:31:3:27,3,0 1/1:4,28:32:9:76,9,0 1/1:6,25:32:3:25,3,0 1 28835 . A G 35.58 HARD_TO_VALIDATE;LowQD;LowQual AC=4;AF=1.00;AN=4;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=5.96;MQ0=60;QD=0.96 GT:AD:DP:GQ:PL ./. ./. 1/1:8,14:22:3:27,3,0 1/1:7,8:15:3:32,3,0 1 29368 . G A 35.79 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=2.900;DP=106;Dels=0.00;FS=14.782;HaplotypeScore=0.4967;MLEAC=3;MLEAF=0.375;MQ=14.44;MQ0=66;MQRankSum=-1.538;QD=0.44;ReadPosRankSum=-2.355 GT:AD:DP:GQ:PL 0/1:24,3:27:10:10,0,124 0/0:18,5:23:5:0,5,190 0/1:25,10:35:50:50,0,147 0/1:16,4:20:7:7,0,142 1 30548 . T G 413.72 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=-4.559;DP=241;Dels=0.00;FS=0.000;HaplotypeScore=1.3235;MLEAC=8;MLEAF=1.00;MQ=10.91;MQ0=190;MQRankSum=2.879;QD=1.72;ReadPosRankSum=0.605 GT:AD:DP:GQ:PL 1/1:37,15:54:6:56,6,0 1/1:29,31:61:18:154,18,0 0/1:38,28:66:3:150,0,3 1/1:30,29:59:9:80,9,0 1 30923 . G T 303.38 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=108;Dels=0.05;FS=0.000;HaplotypeScore=2.2909;MLEAC=8;MLEAF=1.00;MQ=12.79;MQ0=13;QD=2.81 GT:AD:DP:GQ:PL 1/1:0,24:24:9:84,9,0 1/1:0,25:26:3:33,3,0 1/1:0,26:26:6:70,6,0 1/1:0,27:27:15:141,15,0 1 31029 . G A 179.31 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.2400;MLEAC=6;MLEAF=1.00;MQ=9.54;MQ0=54;QD=3.59 GT:AD:DP:GQ:PL ./. 1/1:17,3:20:9:90,9,0 1/1:10,4:14:6:65,6,0 1/1:13,3:16:6:49,6,0 1 39255 . A C 530.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.954;DP=200;Dels=0.00;FS=15.994;HaplotypeScore=0.7440;MLEAC=4;MLEAF=0.500;MQ=11.39;MQ0=142;MQRankSum=0.233;QD=2.65;ReadPosRankSum=-1.632 GT:AD:DP:GQ:PL 0/1:30,23:53:99:193,0,101 0/1:30,18:49:82:82,0,167 0/1:22,22:44:33:144,0,33 0/1:26,28:54:57:144,0,57 1 39261 . T C 478.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.993;DP=207;Dels=0.00;FS=13.616;HaplotypeScore=1.1063;MLEAC=4;MLEAF=0.500;MQ=10.82;MQ0=152;MQRankSum=-0.322;QD=2.31;ReadPosRankSum=-1.140 GT:AD:DP:GQ:PL 0/1:29,27:56:99:167,0,104 0/1:28,20:48:99:108,0,134 0/1:19,24:43:36:117,0,36 0/1:28,31:60:63:119,0,63 1 39292 . G T 49.97 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-1.646;DP=239;Dels=0.00;FS=0.000;HaplotypeScore=0.5615;MLEAC=2;MLEAF=0.250;MQ=8.86;MQ0=198;MQRankSum=0.502;QD=0.54;ReadPosRankSum=0.780 GT:AD:DP:GQ:PL 0/0:59,11:70:6:0,6,278 0/1:34,8:42:62:62,0,121 0/1:43,7:50:21:21,0,48 0/0:68,8:76:21:0,21,198 1 39406 . G C 61.11 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.384;DP=256;Dels=0.00;FS=0.000;HaplotypeScore=0.7450;MLEAC=2;MLEAF=0.250;MQ=9.59;MQ0=210;MQRankSum=-0.858;QD=0.30;ReadPosRankSum=0.083 GT:AD:DP:GQ:PL 0/0:51,4:55:24:0,24,224 0/1:65,7:72:1:1,0,195 0/1:54,11:65:84:87,0,84 0/1:59,5:64:2:2,0,371 1 39423 . T C 63.33 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-4.034;DP=263;Dels=0.00;FS=0.000;HaplotypeScore=1.0001;MLEAC=2;MLEAF=0.250;MQ=10.82;MQ0=202;MQRankSum=-2.098;QD=0.47;ReadPosRankSum=-0.098 GT:AD:DP:GQ:PL 0/1:38,15:53:78:78,0,160 0/1:67,15:82:19:19,0,238 0/0:59,8:67:11:0,11,303 0/0:49,10:59:57:0,57,533 1 39874 . C T 100.95 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.245;DP=235;Dels=0.00;FS=0.000;HaplotypeScore=0.1972;MLEAC=3;MLEAF=0.375;MQ=8.44;MQ0=200;MQRankSum=-0.472;QD=0.59;ReadPosRankSum=0.510 GT:AD:DP:GQ:PL 0/0:63,1:64:27:0,27,250 0/1:50,6:56:65:65,0,91 0/1:51,6:57:18:40,0,18 0/1:53,5:58:30:30,0,172 1 47960 . T A 381.78 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=109;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=8.98;MQ0=94;QD=3.50 GT:AD:DP:GQ:PL 1/1:14,13:27:12:118,12,0 1/1:12,16:28:9:89,9,0 1/1:18,11:29:9:89,9,0 1/1:14,9:23:12:111,12,0 1 48448 . C T 417.50 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=1.369;DP=195;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=7.35;MQ0=176;MQRankSum=0.274;QD=2.14;ReadPosRankSum=1.187 GT:AD:DP:GQ:PL 1/1:38,8:46:3:30,3,0 1/1:48,10:58:18:174,18,0 0/1:43,15:58:12:130,0,12 1/1:23,10:33:12:113,12,0 1 49291 . C T 64.79 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=11.83;MQ0=10;QD=5.89 GT:AD:DP:GQ:PL 1/1:2,2:4:3:32,3,0 1/1:0,2:2:3:24,3,0 1/1:3,2:5:3:32,3,0 ./. 1 49404 . C A 305.03 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=9.72;MQ0=73;QD=3.32 GT:AD:DP:GQ:PL 1/1:9,7:18:9:91,9,0 1/1:10,14:27:9:91,9,0 1/1:13,7:21:3:32,3,0 1/1:10,14:25:15:152,15,0 1 49427 . C T 140.37 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=0.724;DP=99;Dels=0.00;FS=3.485;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=11.67;MQ0=70;MQRankSum=-1.864;QD=1.73;ReadPosRankSum=-0.724 GT:AD:DP:GQ:PL 0/0:15,3:18:6:0,6,61 0/1:21,9:30:73:73,0,73 0/1:18,6:24:41:41,0,51 0/1:20,6:27:59:59,0,128 1 49448 . A G 185.46 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=-0.898;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=0.3670;MLEAC=5;MLEAF=0.625;MQ=11.04;MQ0=65;MQRankSum=0.558;QD=2.02;ReadPosRankSum=-3.276 GT:AD:DP:GQ:PL 1/1:13,8:21:3:30,3,0 0/1:17,11:28:41:41,0,99 0/1:14,6:20:41:49,0,41 0/1:13,10:23:62:97,0,62 1 51898 . C A 165.18 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=19.14;MQ0=5;QD=12.71 GT:AD:DP:GQ:PL 1/1:0,4:4:6:64,6,0 1/1:0,5:5:3:32,3,0 1/1:0,2:2:3:30,3,0 1/1:0,2:2:6:63,6,0 1 51928 . G A 343.93 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=22.64;MQ0=5;QD=16.38 GT:AD:DP:GQ:PL 1/1:0,5:5:9:97,9,0 1/1:0,8:8:9:85,9,0 1/1:0,4:4:9:94,9,0 1/1:0,4:4:9:93,9,0 1 52238 . T G 573.66 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.614;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.8083;MLEAC=8;MLEAF=1.00;MQ=28.12;MQ0=0;MQRankSum=-1.494;QD=19.12;ReadPosRankSum=-1.255 GT:AD:DP:GQ:PL 1/1:1,4:6:9:100,9,0 1/1:0,10:10:18:187,18,0 1/1:0,9:9:21:224,21,0 1/1:0,5:5:9:88,9,0 1 54001 . A G 200.68 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=13.94;MQ0=15;QD=8.73 GT:AD:DP:GQ:PL 1/1:2,3:5:6:59,6,0 1/1:1,8:9:3:24,3,0 1/1:0,3:3:6:53,6,0 1/1:3,3:6:9:89,9,0 1 54366 . A G 40.58 HARD_TO_VALIDATE;LowQual AC=4;AF=1.00;AN=4;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=16.38;MQ0=6;QD=10.14 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:34,3,0 1/1:1,2:3:3:30,3,0 1 54586 . T C 435.19 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=29.73;MQ0=4;QD=19.78 GT:AD:DP:GQ:PL 1/1:0,3:4:3:35,3,0 1/1:0,7:7:9:105,9,0 1/1:0,4:4:9:80,9,0 1/1:0,7:7:21:240,21,0 1 54676 . C T 475.06 PASS AC=8;AF=1.00;AN=8;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=42.50;MQ0=2;QD=22.62 GT:AD:DP:GQ:PL 1/1:0,6:6:9:102,9,0 1/1:0,2:2:6:65,6,0 1/1:0,4:4:6:73,6,0 1/1:0,9:9:24:260,24,0 1 54708 . G C 475.99 PASS AC=8;AF=1.00;AN=8;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=3.0597;MLEAC=8;MLEAF=1.00;MQ=43.98;MQ0=2;QD=20.70 GT:AD:DP:GQ:PL 1/1:0,5:5:6:69,6,0 1/1:0,4:4:6:68,6,0 1/1:0,5:5:12:135,12,0 1/1:0,8:9:21:229,21,0 1 54716 . C T 194.19 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.137;DP=28;Dels=0.04;FS=13.415;HaplotypeScore=2.8889;MLEAC=4;MLEAF=0.500;MQ=46.77;MQ0=2;MQRankSum=-1.889;QD=10.22;ReadPosRankSum=1.068 GT:AD:DP:GQ:PL 0/1:1,5:6:15:61,0,15 1/1:0,3:3:6:68,6,0 0/1:5,5:10:99:101,0,148 0/0:8,0:8:21:0,21,239 1 54720 . C T 36.08 LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=-1.856;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.9671;MLEAC=3;MLEAF=0.375;MQ=48.54;MQ0=2;MQRankSum=-0.442;QD=1.64;ReadPosRankSum=-2.386 GT:AD:DP:GQ:PL 0/1:6,1:7:22:22,0,81 0/1:3,1:4:15:15,0,60 0/0:11,0:11:30:0,30,349 0/1:9,2:11:33:33,0,244 1 54844 . G A 581.72 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=17.74;MQ0=48;QD=8.08 GT:AD:DP:GQ:PL 1/1:8,9:17:12:125,12,0 1/1:9,6:15:6:59,6,0 1/1:10,10:20:24:243,24,0 1/1:10,10:20:18:180,18,0 1 55085 . T A 637.49 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=20.01;MQ0=33;QD=10.99 GT:AD:DP:GQ:PL 1/1:11,5:16:12:125,12,0 1/1:4,8:12:18:194,18,0 1/1:6,6:12:15:162,15,0 1/1:7,11:18:18:182,18,0 1 55164 . C A 34.33 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=12.32;MQ0=12;QD=6.87 GT:AD:DP:GQ:PL ./. ./. 1/1:0,5:5:6:59,6,0 ./. 1 56799 . T C 36.58 LowQual AC=4;AF=1.00;AN=4;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=16.27;MQ0=1;QD=9.15 GT:AD:DP:GQ:PL 1/1:0,2:2:3:30,3,0 ./. ./. 1/1:0,2:2:3:30,3,0 1 57246 . C G 133.08 PASS AC=6;AF=1.00;AN=6;BaseQRankSum=0.736;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.2774;MLEAC=6;MLEAF=1.00;MQ=25.13;MQ0=1;MQRankSum=0.736;QD=19.01;ReadPosRankSum=-0.736 GT:AD:DP:GQ:PL 1/1:0,1:1:3:33,3,0 1/1:1,2:3:3:30,3,0 ./. 1/1:0,3:3:9:94,9,0 1 57376 . C T 123.18 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=14.94;MQ0=9;QD=13.69 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:59,6,0 1/1:0,7:7:9:89,9,0 ./. 1 57483 . G A 241.59 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=8.28;MQ0=72;QD=2.95 GT:AD:DP:GQ:PL 1/1:16,5:21:6:59,6,0 1/1:11,8:20:12:118,12,0 1/1:16,1:17:3:30,3,0 1/1:19,5:24:6:59,6,0 1 57856 . T A 835.44 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=17.70;MQ0=41;QD=11.29 GT:AD:DP:GQ:PL 1/1:7,10:17:21:217,21,0 1/1:10,4:14:12:118,12,0 1/1:14,12:26:27:266,27,0 1/1:6,11:17:24:260,24,0 1 58211 . A G 188.56 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;BaseQRankSum=0.747;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=21.88;MQ0=4;MQRankSum=0.747;QD=18.86;ReadPosRankSum=-0.747 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 1/1:0,2:2:3:30,3,0 ./. 1/1:1,5:6:12:124,12,0 1 58771 . T C 669.53 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=0.2489;MLEAC=8;MLEAF=1.00;MQ=16.12;MQ0=56;QD=8.07 GT:AD:DP:GQ:PL 1/1:16,9:25:12:133,12,0 1/1:8,8:16:15:152,15,0 1/1:12,6:18:12:127,12,0 1/1:12,12:24:27:283,27,0 1 58866 . C G 913.62 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=143;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=12.19;MQ0=107;QD=6.39 GT:AD:DP:GQ:PL 1/1:16,13:29:24:267,24,0 1/1:26,15:41:30:294,30,0 1/1:21,6:27:6:53,6,0 1/1:32,14:46:33:325,33,0 1 58989 . C G 61 HARD_TO_VALIDATE;LowQD AC=4;AF=1.00;AN=4;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=4.25;MQ0=101;QD=1.07 GT:AD:DP:GQ:PL 1/1:22,5:27:6:55,6,0 ./. ./. 1/1:24,6:30:3:30,3,0 1 60332 . T C 772.46 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.2080;MLEAC=8;MLEAF=1.00;MQ=15.01;MQ0=46;QD=9.78 GT:AD:DP:GQ:PL 1/1:11,11:22:15:148,15,0 1/1:8,12:20:24:231,24,0 1/1:9,6:15:12:123,12,0 1/1:9,13:22:30:296,30,0 1 61219 . T C 74 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=7.72;MQ0=63;QD=1.85 GT:AD:DP:GQ:PL 1/1:12,2:15:6:68,6,0 ./. ./. 1/1:21,4:25:3:30,3,0 1 61442 . A G 38.58 HARD_TO_VALIDATE;LowQual AC=4;AF=1.00;AN=4;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.4995;MLEAC=4;MLEAF=1.00;MQ=16.42;MQ0=7;QD=5.51 GT:AD:DP:GQ:PL ./. ./. 1/1:0,3:3:3:30,3,0 1/1:0,4:4:3:32,3,0 1 61499 . G A 105.33 PASS AC=6;AF=1.00;AN=6;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=25.22;MQ0=2;QD=26.33 GT:AD:DP:GQ:PL 1/1:0,1:1:3:30,3,0 1/1:0,2:2:6:64,6,0 1/1:0,1:1:3:35,3,0 ./. 1 61851 . T A 318.81 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.470;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=28.50;MQ0=2;MQRankSum=0.401;QD=21.25;ReadPosRankSum=0.668 GT:AD:DP:GQ:PL 1/1:1,3:4:6:72,6,0 1/1:0,1:1:3:30,3,0 1/1:0,2:2:3:24,3,0 1/1:0,8:8:21:217,21,0 1 61987 . A G 953.43 PASS AC=8;AF=1.00;AN=8;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.2495;MLEAC=8;MLEAF=1.00;MQ=50.78;MQ0=2;QD=27.24 GT:AD:DP:GQ:PL 1/1:1,10:12:24:267,24,0 1/1:0,9:9:24:270,24,0 1/1:0,4:4:12:145,12,0 1/1:1,9:10:27:297,27,0 1 61989 . G C 1034.43 PASS AC=8;AF=1.00;AN=8;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.1446;MLEAC=8;MLEAF=1.00;MQ=50.33;MQ0=2;QD=28.73 GT:AD:DP:GQ:PL 1/1:1,11:12:24:279,24,0 1/1:0,10:10:27:320,27,0 1/1:0,4:4:12:144,12,0 1/1:1,9:10:27:317,27,0 1 62203 . T C 1014.53 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=34.05;MQ0=4;QD=26.01 GT:AD:DP:GQ:PL 1/1:0,11:11:27:296,27,0 1/1:0,6:6:9:92,9,0 1/1:0,6:6:15:175,15,0 1/1:0,16:16:45:477,45,0 1 62271 . A G 240.11 PASS AC=6;AF=1.00;AN=6;BaseQRankSum=0.348;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.2447;MLEAC=6;MLEAF=1.00;MQ=26.44;MQ0=3;MQRankSum=1.044;QD=18.47;ReadPosRankSum=-1.393 GT:AD:DP:GQ:PL ./. 1/1:1,5:6:9:96,9,0 1/1:1,2:3:6:66,6,0 1/1:0,4:4:9:103,9,0 1 62777 . A T 363.51 HARD_TO_VALIDATE AC=5;AF=0.833;AN=6;BaseQRankSum=0.306;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.833;MQ=13.42;MQ0=40;MQRankSum=-1.531;QD=7.13;ReadPosRankSum=-1.531 GT:AD:DP:GQ:PL 1/1:11,7:19:12:125,12,0 0/1:10,10:20:6:183,0,6 1/1:6,6:12:9:83,9,0 ./. 1 63516 . A G 87.68 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=11.65;MQ0=14;QD=7.31 GT:AD:DP:GQ:PL ./. 1/1:2,3:5:3:32,3,0 ./. 1/1:2,5:7:9:80,9,0 1 63527 . T C 90.68 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=12.76;MQ0=11;QD=9.07 GT:AD:DP:GQ:PL ./. 1/1:2,3:5:3:30,3,0 ./. 1/1:1,4:5:9:85,9,0 1 64548 . A C 212.95 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=-0.107;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=9.02;MQ0=94;MQRankSum=-0.107;QD=2.01;ReadPosRankSum=0.322 GT:AD:DP:GQ:PL 1/1:30,2:32:6:61,6,0 0/1:23,3:26:26:27,0,26 1/1:16,8:24:9:89,9,0 1/1:21,3:24:6:66,6,0 1 64552 . G A 207.93 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=-2.256;DP=110;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=8.85;MQ0=98;MQRankSum=-0.107;QD=1.89;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 1/1:29,2:31:6:61,6,0 0/1:26,4:30:26:26,0,31 1/1:16,8:24:9:89,9,0 1/1:21,4:25:6:62,6,0 1 65797 . T C 161.33 HARD_TO_VALIDATE;LowQD AC=8;AF=1.00;AN=8;DP=137;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=5.52;MQ0=130;QD=1.18 GT:AD:DP:GQ:PL 1/1:31,6:37:3:32,3,0 1/1:24,6:30:3:26,3,0 1/1:27,3:30:3:32,3,0 1/1:33,7:40:9:95,9,0 1 65872 . T G 504.84 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=134;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=9.65;MQ0=116;QD=3.77 GT:AD:DP:GQ:PL 1/1:24,12:36:12:126,12,0 1/1:23,6:29:6:63,6,0 1/1:26,4:30:9:95,9,0 1/1:24,14:38:24:246,24,0 1 66162 . A T 262.51 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=-0.791;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=28.16;MQ0=0;MQRankSum=1.423;QD=23.86;ReadPosRankSum=-0.474 GT:AD:DP:GQ:PL 1/1:0,3:3:9:95,9,0 1/1:0,1:1:3:32,3,0 1/1:1,2:3:6:63,6,0 1/1:0,4:4:9:97,9,0 1 66378 . A T 31.40 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=2.9320;MLEAC=1;MLEAF=0.500;MQ=29.36;MQ0=3;MQRankSum=0.736;QD=10.47;ReadPosRankSum=0.736 GT:AD:DP:GQ:PL 0/1:1,2:3:20:57,0,20 ./. ./. ./. 1 66577 . A C 40.58 LowQual AC=4;AF=1.00;AN=4;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=15.64;MQ0=3;QD=8.12 GT:AD:DP:GQ:PL ./. 1/1:1,1:2:3:32,3,0 ./. 1/1:1,2:3:3:32,3,0 1 71875 . G A 92.33 HARD_TO_VALIDATE;LowQD AC=6;AF=1.00;AN=6;DP=87;Dels=0.00;FS=0.000;HaplotypeScore=0.5075;MLEAC=6;MLEAF=1.00;MQ=5.31;MQ0=83;QD=1.36 GT:AD:DP:GQ:PL 1/1:14,6:20:3:30,3,0 ./. 1/1:14,5:19:6:58,6,0 1/1:22,7:29:3:28,3,0 1 72862 . G A 246.41 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=0.6913;MLEAC=6;MLEAF=0.750;MQ=8.36;MQ0=82;QD=2.59 GT:AD:DP:GQ:PL 1/1:19,8:28:12:103,12,0 1/1:15,4:19:3:29,3,0 1/1:7,7:14:3:29,3,0 1/1:25,8:34:15:143,15,0 1 72893 . T C 367.93 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=8.84;MQ0=86;QD=3.68 GT:AD:DP:GQ:PL 1/1:17,5:22:9:79,9,0 1/1:22,5:27:9:86,9,0 1/1:13,5:18:6:57,6,0 1/1:27,6:33:18:171,18,0 1 74570 . T A 73.84 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.053;DP=210;Dels=0.00;FS=0.000;HaplotypeScore=1.5334;MLEAC=4;MLEAF=0.500;MQ=4.80;MQ0=192;MQRankSum=2.920;QD=0.75;ReadPosRankSum=-2.920 GT:AD:DP:GQ:PL 0/0:55,0:55:3:0,3,22 1/1:43,2:46:6:58,6,0 0/1:50,2:52:13:48,0,13 0/0:55,1:56:3:0,3,22 1 74681 . G T 642.46 HARD_TO_VALIDATE AC=6;AF=0.750;AN=8;BaseQRankSum=-0.347;DP=79;Dels=0.01;FS=27.597;HaplotypeScore=0.7153;MLEAC=6;MLEAF=0.750;MQ=19.39;MQ0=43;MQRankSum=3.670;QD=8.13;ReadPosRankSum=-0.639 GT:AD:DP:GQ:PL 0/1:20,5:25:7:119,0,7 1/1:8,5:13:15:166,15,0 1/1:10,11:21:8:267,8,0 0/1:13,6:19:7:121,0,7 1 74764 . A T 60.85 HARD_TO_VALIDATE AC=2;AF=0.500;AN=4;BaseQRankSum=0.550;DP=57;Dels=0.00;FS=3.979;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.500;MQ=9.75;MQ0=47;MQRankSum=0.937;QD=2.10;ReadPosRankSum=0.550 GT:AD:DP:GQ:PL 0/1:14,3:17:13:63,0,13 ./. 0/1:10,2:12:16:25,0,16 ./. 1 74771 . A G 61.78 HARD_TO_VALIDATE AC=3;AF=0.750;AN=4;BaseQRankSum=-1.380;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.750;MQ=10.02;MQ0=42;MQRankSum=0.720;QD=2.57;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL 1/1:10,3:13:6:63,6,0 ./. 0/1:9,2:11:16:26,0,16 ./. 1 75139 . C G 211.68 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.423;DP=141;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=6.46;MQ0=130;MQRankSum=0.791;QD=1.50;ReadPosRankSum=-1.107 GT:AD:DP:GQ:PL 1/1:43,2:45:6:60,6,0 1/1:30,4:35:9:83,9,0 1/1:29,2:31:3:29,3,0 1/1:26,4:30:6:64,6,0 1 75194 . G C 96.92 HARD_TO_VALIDATE;LowQD AC=8;AF=1.00;AN=8;BaseQRankSum=1.067;DP=117;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=5.82;MQ0=109;MQRankSum=1.067;QD=0.83;ReadPosRankSum=0.572 GT:AD:DP:GQ:PL 1/1:28,2:30:3:29,3,0 1/1:27,2:29:3:30,3,0 1/1:32,1:33:3:32,3,0 1/1:23,2:25:3:29,3,0 1 94260 . G A 225.82 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=8.30;MQ0=52;QD=3.58 GT:AD:DP:GQ:PL 1/1:8,12:20:18:148,18,0 1/1:8,6:14:6:48,6,0 1/1:7,7:14:3:27,3,0 1/1:7,8:15:3:27,3,0 1 94545 . C T 308.08 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.272;DP=108;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=8.20;MQ0=89;MQRankSum=3.377;QD=2.85;ReadPosRankSum=0.921 GT:AD:DP:GQ:PL 1/1:32,9:41:18:162,18,0 1/1:16,6:22:9:73,9,0 1/1:19,5:24:6:51,6,0 1/1:15,6:21:6:47,6,0 1 94699 . G A 50 HARD_TO_VALIDATE;LowQD AC=4;AF=1.00;AN=4;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=3.97;MQ0=72;QD=1.02 GT:AD:DP:GQ:PL 1/1:19,3:22:3:25,3,0 1/1:23,4:27:6:49,6,0 ./. ./. 1 94893 . A G 34.58 HARD_TO_VALIDATE;LowQual AC=4;AF=1.00;AN=4;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=12.23;MQ0=7;QD=3.84 GT:AD:DP:GQ:PL 1/1:0,5:5:3:25,3,0 1/1:0,4:4:3:33,3,0 ./. ./. 1 98033 . G C 156.96 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.457;DP=169;Dels=0.00;FS=3.861;HaplotypeScore=0.2416;MLEAC=4;MLEAF=0.500;MQ=9.18;MQ0=129;MQRankSum=1.402;QD=0.93;ReadPosRankSum=-0.339 GT:AD:DP:GQ:PL 0/1:38,5:43:35:35,0,58 0/1:36,10:46:96:100,0,96 0/1:30,5:35:27:27,0,156 0/1:41,4:45:27:27,0,106 1 98945 . C T 68 PASS AC=4;AF=1.00;AN=4;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=26.06;MQ0=0;QD=22.67 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 ./. ./. 1/1:0,1:1:3:33,3,0 1 98993 . G A 116.23 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.639;DP=18;Dels=0.00;FS=2.112;HaplotypeScore=3.4327;MLEAC=4;MLEAF=0.500;MQ=45.35;MQ0=0;MQRankSum=-0.421;QD=7.26;ReadPosRankSum=1.171 GT:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,32 1/1:2,2:4:6:67,6,0 0/1:4,2:6:24:24,0,77 0/1:4,2:6:58:58,0,88 1 101268 . G A 184.29 HARD_TO_VALIDATE AC=6;AF=0.750;AN=8;BaseQRankSum=1.090;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=10.18;MQ0=69;MQRankSum=1.246;QD=3.18;ReadPosRankSum=-1.401 GT:AD:DP:GQ:PL 1/1:13,5:18:6:69,6,0 0/0:21,4:25:3:0,3,33 1/1:13,2:15:6:50,6,0 1/1:13,12:25:9:97,9,0 1 101389 . A C 172.13 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=0.204;DP=109;Dels=0.00;FS=0.000;HaplotypeScore=0.6778;MLEAC=3;MLEAF=0.375;MQ=19.65;MQ0=65;MQRankSum=-0.436;QD=2.00;ReadPosRankSum=-1.426 GT:AD:DP:GQ:PL 0/1:25,3:28:14:14,0,136 0/1:17,5:22:99:105,0,165 0/1:31,5:36:87:87,0,344 0/0:23,0:23:21:0,21,233 1 102138 . C T 169.20 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=13.91;MQ0=7;QD=11.28 GT:AD:DP:GQ:PL 1/1:2,6:8:12:98,12,0 ./. 1/1:0,3:3:6:49,6,0 1/1:0,4:4:6:47,6,0 1 102664 . A G 759.54 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=17.85;MQ0=58;QD=9.15 GT:AD:DP:GQ:PL 1/1:11,8:19:9:107,9,0 1/1:12,10:22:24:278,24,0 1/1:8,11:19:15:174,15,0 1/1:12,11:23:21:226,21,0 1 103241 . C T 935.40 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.6934;MLEAC=8;MLEAF=1.00;MQ=21.45;MQ0=32;QD=13.17 GT:AD:DP:GQ:PL 1/1:3,7:10:15:153,15,0 1/1:6,11:17:21:225,21,0 1/1:4,19:23:27:279,27,0 1/1:2,19:21:30:304,30,0 1 103250 . G A 382.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.184;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.4776;MLEAC=4;MLEAF=0.500;MQ=22.23;MQ0=27;MQRankSum=0.687;QD=5.89;ReadPosRankSum=0.453 GT:AD:DP:GQ:PL 0/1:6,4:10:38:107,0,38 0/1:11,5:16:77:83,0,77 0/1:7,13:20:64:165,0,64 0/1:12,7:19:60:60,0,175 1 104033 . T C 977.37 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.3807;MLEAC=8;MLEAF=1.00;MQ=16.59;MQ0=31;QD=12.37 GT:AD:DP:GQ:PL 1/1:4,11:16:24:216,24,0 1/1:6,17:23:33:302,33,0 1/1:0,18:18:24:244,24,0 1/1:2,20:22:24:241,24,0 1 105550 . G A 30.08 HARD_TO_VALIDATE;LowQD;LowQual AC=4;AF=0.667;AN=6;BaseQRankSum=0.736;DP=106;Dels=0.00;FS=4.771;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=3.78;MQ0=103;MQRankSum=0.736;QD=0.58;ReadPosRankSum=0.736 GT:AD:DP:GQ:PL 1/1:18,2:20:3:29,3,0 ./. 1/1:27,5:32:3:29,3,0 0/0:24,3:27:3:0,3,24 1 108365 . A G 255.54 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.8564;MLEAC=8;MLEAF=1.00;MQ=16.51;MQ0=9;QD=10.65 GT:AD:DP:GQ:PL 1/1:0,3:4:3:28,3,0 1/1:1,5:6:6:57,6,0 1/1:1,4:5:6:52,6,0 1/1:1,8:9:15:143,15,0 1 108893 . C T 921.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.480;DP=170;Dels=0.00;FS=0.840;HaplotypeScore=0.8719;MLEAC=4;MLEAF=0.500;MQ=20.61;MQ0=67;MQRankSum=-2.043;QD=5.42;ReadPosRankSum=-0.977 GT:AD:DP:GQ:PL 0/1:24,13:37:99:176,0,312 0/1:29,18:47:99:320,0,249 0/1:22,14:36:99:166,0,268 0/1:33,17:50:99:292,0,357 1 109640 . T A 451.71 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=33.63;MQ0=7;QD=14.12 GT:AD:DP:GQ:PL 1/1:0,10:10:12:127,12,0 1/1:0,5:5:12:128,12,0 1/1:0,9:9:9:86,9,0 1/1:0,8:8:12:136,12,0 1 111735 . C A 46.60 HARD_TO_VALIDATE;LowQD;LowQual AC=4;AF=0.500;AN=8;BaseQRankSum=-0.676;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=5.42;MQ0=88;MQRankSum=1.098;QD=0.70;ReadPosRankSum=0.103 GT:AD:DP:GQ:PL 0/1:20,4:24:33:36,0,33 0/0:30,1:31:3:0,3,24 0/1:19,2:21:17:18,0,17 1/1:20,2:22:3:24,3,0 1 112021 . G A 235.02 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.356;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=8.82;MQ0=93;MQRankSum=-0.246;QD=1.99;ReadPosRankSum=-0.246 GT:AD:DP:GQ:PL 0/1:25,4:29:71:71,0,94 0/1:31,3:35:16:39,0,16 0/1:25,6:31:30:79,0,30 0/1:18,5:23:30:78,0,30 1 112326 . A C 151.03 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-2.094;DP=153;Dels=0.00;FS=0.000;HaplotypeScore=0.2447;MLEAC=4;MLEAF=0.500;MQ=7.36;MQ0=128;MQRankSum=-2.257;QD=0.99;ReadPosRankSum=0.354 GT:AD:DP:GQ:PL 0/1:27,3:30:17:17,0,19 0/1:34,10:44:68:68,0,70 0/1:32,9:41:50:50,0,55 0/1:28,9:37:48:48,0,77 1 113682 . A G 152.93 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.818;DP=160;Dels=0.00;FS=11.685;HaplotypeScore=0.4413;MLEAC=3;MLEAF=0.375;MQ=8.77;MQ0=119;MQRankSum=2.302;QD=1.19;ReadPosRankSum=0.151 GT:AD:DP:GQ:PL 0/1:46,11:57:67:90,0,67 0/1:32,8:40:26:26,0,95 0/0:29,2:31:27:0,27,204 0/1:22,9:31:69:71,0,69 1 113969 . C T 156.31 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=10.87;MQ0=28;QD=4.74 GT:AD:DP:GQ:PL ./. 1/1:5,8:13:6:49,6,0 1/1:3,4:7:9:73,9,0 1/1:4,9:13:6:59,6,0 1 114810 . C T 277.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=9.36;MQ0=44;QD=4.33 GT:AD:DP:GQ:PL 1/1:9,11:20:18:152,18,0 1/1:9,5:14:6:51,6,0 1/1:5,7:12:3:25,3,0 1/1:7,11:18:9:74,9,0 1 115902 . T A 300.02 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.638;DP=175;Dels=0.00;FS=0.000;HaplotypeScore=0.2498;MLEAC=4;MLEAF=0.500;MQ=11.67;MQ0=150;MQRankSum=0.305;QD=1.71;ReadPosRankSum=1.193 GT:AD:DP:GQ:PL 0/1:29,3:32:30:30,0,31 0/1:34,8:42:19:126,0,19 0/1:44,7:51:19:29,0,19 0/1:40,10:50:48:147,0,48 1 118318 . A G 179.47 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=1.625;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=9.59;MQ0=96;MQRankSum=-0.567;QD=2.11;ReadPosRankSum=0.567 GT:AD:DP:GQ:PL 0/0:29,2:31:6:0,6,57 0/1:18,7:25:54:85,0,54 0/1:23,14:37:28:111,0,28 0/1:21,2:23:16:16,0,38 1 118617 . T C 1736.36 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.565;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=0.8575;MLEAC=8;MLEAF=1.00;MQ=20.13;MQ0=3;MQRankSum=0.397;QD=20.19;ReadPosRankSum=0.856 GT:AD:DP:GQ:PL 1/1:1,21:22:28:360,28,0 1/1:0,24:24:66:567,66,0 1/1:0,17:17:45:384,45,0 1/1:0,23:23:57:451,57,0 1 121009 . C T 127.91 PASS AC=6;AF=1.00;AN=6;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=47.48;MQ0=1;QD=21.32 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:64,6,0 1/1:0,1:1:3:29,3,0 1/1:0,3:3:6:59,6,0 1 122872 . T G 1040.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.428;DP=126;Dels=0.00;FS=1.530;HaplotypeScore=0.3943;MLEAC=4;MLEAF=0.500;MQ=24.15;MQ0=9;MQRankSum=0.842;QD=8.26;ReadPosRankSum=-0.630 GT:AD:DP:GQ:PL 0/1:19,16:35:99:297,0,341 0/1:16,17:33:99:335,0,274 0/1:19,14:33:99:238,0,306 0/1:12,13:25:99:203,0,175 1 123143 . C G 180.97 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.741;DP=146;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=9.66;MQ0=125;MQRankSum=2.096;QD=1.24;ReadPosRankSum=-0.533 GT:AD:DP:GQ:PL 0/1:25,5:30:34:83,0,34 0/1:37,4:41:42:42,0,47 0/1:42,5:47:66:66,0,83 0/1:23,5:28:22:22,0,24 1 123511 . G A 1085.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=140;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=11.36;MQ0=94;QD=7.75 GT:AD:DP:GQ:PL 1/1:14,13:27:30:247,30,0 1/1:23,15:38:39:321,39,0 1/1:21,12:33:27:222,27,0 1/1:25,17:42:39:321,39,0 1 123642 . T G 246.81 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=154;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=5.01;MQ0=142;QD=1.60 GT:AD:DP:GQ:PL 1/1:35,7:42:3:23,3,0 1/1:31,15:46:24:178,24,0 1/1:25,6:31:6:48,6,0 1/1:26,9:35:3:22,3,0 1 125976 . C T 30.33 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.48;MQ0=4;QD=10.11 GT:AD:DP:GQ:PL ./. 1/1:0,3:3:6:55,6,0 ./. ./. 1 126113 . C A 917.38 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=24.30;MQ0=9;QD=19.52 GT:AD:DP:GQ:PL 1/1:0,12:12:30:254,30,0 1/1:0,7:7:21:184,21,0 1/1:0,11:11:18:174,18,0 1/1:0,17:17:33:331,33,0 1 127219 . A C 86.96 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.872;DP=143;Dels=0.00;FS=0.000;HaplotypeScore=0.2458;MLEAC=3;MLEAF=0.375;MQ=7.01;MQ0=123;MQRankSum=0.951;QD=0.78;ReadPosRankSum=-0.792 GT:AD:DP:GQ:PL 0/0:27,4:31:9:0,9,72 0/1:28,12:40:30:79,0,30 0/1:24,7:31:29:29,0,76 0/1:32,9:41:12:12,0,60 1 127392 . G T 56.84 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.343;DP=146;Dels=0.00;FS=0.000;HaplotypeScore=0.4538;MLEAC=3;MLEAF=0.375;MQ=8.07;MQ0=116;MQRankSum=1.618;QD=0.58;ReadPosRankSum=-1.079 GT:AD:DP:GQ:PL 0/1:32,3:35:51:52,0,51 0/0:45,3:48:6:0,6,181 0/1:24,4:28:9:9,0,78 0/1:32,3:35:28:28,0,76 1 127491 . T G 356.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.810;DP=158;Dels=0.00;FS=20.674;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=17.32;MQ0=61;MQRankSum=1.242;QD=2.26;ReadPosRankSum=2.032 GT:AD:DP:GQ:PL 0/1:31,7:38:31:31,0,289 0/1:31,9:40:99:119,0,379 0/1:32,10:42:99:187,0,448 0/1:33,5:38:52:52,0,298 1 127573 . G A 796.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.617;DP=203;Dels=0.00;FS=2.322;HaplotypeScore=0.6528;MLEAC=4;MLEAF=0.500;MQ=17.48;MQ0=57;MQRankSum=-1.475;QD=3.93;ReadPosRankSum=1.131 GT:AD:DP:GQ:PL 0/1:35,13:48:99:148,0,388 0/1:42,20:62:99:244,0,539 0/1:33,21:54:99:313,0,413 0/1:26,13:39:99:124,0,237 1 127908 . C T 34.15 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=3.194;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.2497;MLEAC=3;MLEAF=0.375;MQ=9.46;MQ0=59;MQRankSum=-0.417;QD=0.58;ReadPosRankSum=1.065 GT:AD:DP:GQ:PL 0/0:20,0:20:3:0,3,23 0/1:20,2:22:27:27,0,73 0/1:13,4:17:31:31,0,53 0/1:18,2:20:7:7,0,83 1 127972 . G A 124.20 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=3.665;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=18.65;MQ0=18;MQRankSum=-2.893;QD=3.27;ReadPosRankSum=-1.350 GT:AD:DP:GQ:PL 0/1:7,2:9:16:16,0,114 0/1:5,5:10:17:17,0,44 0/1:2,7:9:13:87,0,13 0/1:4,6:10:36:36,0,62 1 128274 . A C 55.17 HARD_TO_VALIDATE;LowQD AC=4;AF=0.667;AN=6;BaseQRankSum=0.922;DP=82;Dels=0.00;FS=3.680;HaplotypeScore=0.2217;MLEAC=4;MLEAF=0.667;MQ=8.91;MQ0=74;MQRankSum=-2.017;QD=0.77;ReadPosRankSum=-0.421 GT:AD:DP:GQ:PL ./. 0/1:31,4:35:14:14,0,85 0/1:16,4:20:21:44,0,21 1/1:12,5:17:3:26,3,0 1 128798 . C T 191.75 PASS AC=7;AF=0.875;AN=8;BaseQRankSum=-1.240;DP=18;Dels=0.00;FS=8.451;HaplotypeScore=0.2235;MLEAC=7;MLEAF=0.875;MQ=21.47;MQ0=3;MQRankSum=-0.744;QD=10.65;ReadPosRankSum=-0.248 GT:AD:DP:GQ:PL 1/1:2,6:8:9:90,9,0 1/1:0,2:2:6:56,6,0 0/1:1,3:4:17:50,0,17 1/1:0,4:4:3:25,3,0 1 129285 . G A 1637.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=3.611;DP=137;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=15.04;MQ0=58;MQRankSum=3.590;QD=11.95;ReadPosRankSum=0.877 GT:AD:DP:GQ:PL 1/1:15,27:43:54:467,54,0 1/1:17,18:35:48:425,48,0 1/1:7,17:24:39:338,39,0 1/1:15,20:35:51:433,51,0 1 129315 . A G 628.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.566;DP=132;Dels=0.00;FS=7.578;HaplotypeScore=0.2458;MLEAC=4;MLEAF=0.500;MQ=17.93;MQ0=25;MQRankSum=-0.420;QD=4.76;ReadPosRankSum=0.875 GT:AD:DP:GQ:PL 0/1:19,13:32:99:161,0,241 0/1:27,13:40:99:185,0,311 0/1:16,9:25:99:161,0,138 0/1:22,13:35:99:154,0,299 1 129692 . T A 39.92 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-0.864;DP=213;Dels=0.00;FS=0.000;HaplotypeScore=3.2499;MLEAC=2;MLEAF=0.250;MQ=18.05;MQ0=30;MQRankSum=-2.039;QD=0.37;ReadPosRankSum=1.640 GT:AD:DP:GQ:PL 0/0:45,7:52:25:0,25,603 0/0:43,10:53:37:0,37,553 0/1:50,12:62:38:38,0,651 0/1:42,4:46:36:36,0,463 1 131114 . C T 215.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.387;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=0.7391;MLEAC=4;MLEAF=0.500;MQ=9.29;MQ0=91;MQRankSum=-0.408;QD=1.86;ReadPosRankSum=1.659 GT:AD:DP:GQ:PL 0/1:30,5:35:36:38,0,36 0/1:27,7:34:31:81,0,31 0/1:17,7:24:72:95,0,72 0/1:18,5:23:34:34,0,58 1 131552 . G T 106.05 HARD_TO_VALIDATE;LowQD AC=5;AF=0.833;AN=6;BaseQRankSum=-0.742;DP=163;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.833;MQ=3.91;MQ0=156;MQRankSum=-0.742;QD=0.77;ReadPosRankSum=-0.742 GT:AD:DP:GQ:PL 0/1:47,5:52:17:17,0,18 1/1:41,6:47:6:47,6,0 1/1:35,4:39:9:71,9,0 ./. 1 131609 . C A 44.53 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=2.793;DP=140;Dels=0.00;FS=0.000;HaplotypeScore=0.4958;MLEAC=3;MLEAF=0.375;MQ=6.14;MQ0=128;MQRankSum=-0.380;QD=0.38;ReadPosRankSum=0.689 GT:AD:DP:GQ:PL 0/1:39,5:44:16:16,0,43 0/1:35,5:40:39:41,0,39 0/1:30,3:33:19:20,0,19 0/0:21,2:23:6:0,6,53 1 133010 . C T 232.54 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=16.21;MQ0=4;QD=12.24 GT:AD:DP:GQ:PL 1/1:0,10:10:15:128,15,0 1/1:0,2:2:6:53,6,0 1/1:0,3:3:3:26,3,0 1/1:0,4:4:6:50,6,0 1 133129 . G A 674.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.773;DP=123;Dels=0.00;FS=1.942;HaplotypeScore=1.7465;MLEAC=4;MLEAF=0.500;MQ=30.82;MQ0=30;MQRankSum=-1.393;QD=5.49;ReadPosRankSum=-1.095 GT:AD:DP:GQ:PL 0/1:21,15:36:99:277,0,328 0/1:17,9:26:99:144,0,272 0/1:22,8:30:99:137,0,355 0/1:20,11:31:99:149,0,303 1 133483 . G T 820.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.802;DP=159;Dels=0.00;FS=13.198;HaplotypeScore=1.4575;MLEAC=4;MLEAF=0.500;MQ=23.42;MQ0=65;MQRankSum=-0.787;QD=5.16;ReadPosRankSum=-2.331 GT:AD:DP:GQ:PL 0/1:32,18:50:99:301,0,264 0/1:20,14:34:99:193,0,148 0/1:27,7:34:99:115,0,421 0/1:28,13:41:99:244,0,261 1 135040 . T C 974.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.682;DP=132;Dels=0.00;FS=0.000;HaplotypeScore=1.1223;MLEAC=4;MLEAF=0.500;MQ=23.75;MQ0=28;MQRankSum=-1.138;QD=7.39;ReadPosRankSum=-1.046 GT:AD:DP:GQ:PL 0/1:17,12:31:99:212,0,296 0/1:19,20:39:99:339,0,233 0/1:20,11:31:99:225,0,286 0/1:18,13:31:99:231,0,275 1 136048 . C T 583.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=5.219;DP=85;Dels=0.00;FS=1.199;HaplotypeScore=0.2467;MLEAC=4;MLEAF=0.500;MQ=17.63;MQ0=18;MQRankSum=-1.326;QD=6.87;ReadPosRankSum=-0.007 GT:AD:DP:GQ:PL 0/1:8,12:20:61:142,0,61 0/1:12,12:24:99:163,0,140 0/1:6,11:17:51:130,0,51 0/1:11,13:24:68:181,0,68 1 136505 . A G 38.55 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=-2.048;DP=49;Dels=0.00;FS=1.805;HaplotypeScore=0.8091;MLEAC=3;MLEAF=0.375;MQ=19.99;MQ0=19;MQRankSum=1.063;QD=1.17;ReadPosRankSum=0.181 GT:AD:DP:GQ:PL 0/0:15,1:16:6:0,6,62 0/1:8,1:11:22:22,0,58 0/1:6,3:9:14:14,0,86 0/1:9,3:13:35:35,0,107 1 136506 . C G 92.47 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=1.284;DP=51;Dels=0.00;FS=1.651;HaplotypeScore=0.6645;MLEAC=3;MLEAF=0.375;MQ=20.50;MQ0=19;MQRankSum=1.066;QD=2.72;ReadPosRankSum=-0.849 GT:AD:DP:GQ:PL 0/0:16,1:17:6:0,6,56 0/1:10,1:11:16:16,0,26 0/1:6,4:10:52:66,0,52 0/1:10,3:13:43:43,0,74 1 136603 . A G 106.08 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.817;DP=135;Dels=0.00;FS=1.975;HaplotypeScore=11.0868;MLEAC=3;MLEAF=0.375;MQ=27.05;MQ0=31;MQRankSum=0.050;QD=1.00;ReadPosRankSum=1.329 GT:AD:DP:GQ:PL 0/1:22,8:31:18:18,0,73 0/0:23,6:29:18:0,18,184 0/1:25,12:39:75:75,0,201 0/1:22,12:36:47:47,0,255 1 136652 . A G 113.67 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-3.137;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=10.8689;MLEAC=4;MLEAF=0.500;MQ=19.90;MQ0=34;MQRankSum=0.257;QD=0.96;ReadPosRankSum=-0.011 GT:AD:DP:GQ:PL 0/1:14,8:23:16:16,0,27 0/1:19,12:31:24:24,0,209 0/1:21,5:30:6:6,0,126 0/1:23,9:34:99:99,0,120 1 136787 . G A 118.36 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=2.543;DP=203;Dels=0.00;FS=21.171;HaplotypeScore=6.1903;MLEAC=2;MLEAF=0.250;MQ=29.91;MQ0=34;MQRankSum=0.937;QD=1.30;ReadPosRankSum=-1.662 GT:AD:DP:GQ:PL 0/1:45,5:50:99:99,0,457 0/0:53,6:59:4:0,4,663 0/0:50,3:53:35:0,35,629 0/1:38,3:41:52:52,0,391 1 136817 . T C 148.99 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-5.656;DP=240;Dels=0.00;FS=0.000;HaplotypeScore=4.4363;MLEAC=3;MLEAF=0.375;MQ=26.11;MQ0=48;MQRankSum=1.959;QD=0.77;ReadPosRankSum=-1.428 GT:AD:DP:GQ:PL 0/1:50,11:63:19:19,0,555 0/1:56,13:71:99:102,0,476 0/1:50,10:60:62:62,0,377 0/0:40,5:46:23:0,23,464 1 136877 . G A 108.98 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.956;DP=199;Dels=0.00;FS=0.000;HaplotypeScore=7.7005;MLEAC=3;MLEAF=0.375;MQ=25.65;MQ0=30;MQRankSum=1.314;QD=0.78;ReadPosRankSum=-1.814 GT:AD:DP:GQ:PL 0/1:42,8:50:62:62,0,310 0/0:55,5:60:30:0,30,544 0/1:52,6:59:18:18,0,383 0/1:24,6:30:63:63,0,168 1 136962 . C T 435.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.991;DP=232;Dels=0.00;FS=5.834;HaplotypeScore=6.9853;MLEAC=4;MLEAF=0.500;MQ=24.34;MQ0=55;MQRankSum=0.023;QD=1.88;ReadPosRankSum=0.144 GT:AD:DP:GQ:PL 0/1:48,16:66:99:118,0,327 0/1:41,19:62:99:135,0,237 0/1:42,17:60:77:77,0,307 0/1:26,15:43:99:138,0,146 1 136995 . C T 31.02 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=0.686;DP=196;Dels=0.00;FS=0.000;HaplotypeScore=6.2319;MLEAC=2;MLEAF=0.250;MQ=20.46;MQ0=75;MQRankSum=1.086;QD=0.31;ReadPosRankSum=0.935 GT:AD:DP:GQ:PL 0/1:48,2:50:37:37,0,215 0/0:51,3:59:22:0,22,352 0/1:38,6:50:28:28,0,129 0/0:33,2:37:18:0,18,166 1 137123 . T G 99.03 HARD_TO_VALIDATE AC=5;AF=0.833;AN=6;BaseQRankSum=2.534;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=3.1942;MLEAC=5;MLEAF=0.833;MQ=20.14;MQ0=6;MQRankSum=0.884;QD=5.50;ReadPosRankSum=-0.412 GT:AD:DP:GQ:PL 1/1:4,3:7:6:68,6,0 ./. 1/1:0,3:3:3:34,3,0 0/1:4,4:8:25:25,0,54 1 137287 . G A 30.54 HARD_TO_VALIDATE;LowQD;LowQual AC=4;AF=0.500;AN=8;BaseQRankSum=0.701;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=8.77;MQ0=86;MQRankSum=-0.289;QD=0.41;ReadPosRankSum=1.196 GT:AD:DP:GQ:PL 0/0:31,1:32:9:0,9,86 0/1:17,3:21:17:17,0,87 1/1:24,2:26:3:27,3,0 0/1:21,6:27:20:20,0,72 1 137336 . G A 57.79 HARD_TO_VALIDATE;LowQD AC=6;AF=1.00;AN=6;BaseQRankSum=-1.754;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=4.00;MQ0=93;MQRankSum=1.754;QD=0.78;ReadPosRankSum=1.300 GT:AD:DP:GQ:PL 1/1:22,5:27:3:27,3,0 1/1:18,3:21:3:27,3,0 ./. 1/1:19,7:26:3:27,3,0 1 137622 . G A 205.78 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=3.293;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=0.2395;MLEAC=5;MLEAF=0.625;MQ=9.64;MQ0=88;MQRankSum=1.385;QD=1.85;ReadPosRankSum=-0.954 GT:AD:DP:GQ:PL 0/1:27,4:31:55:55,0,103 0/1:14,7:21:56:56,0,82 0/1:23,7:30:17:46,0,17 1/1:21,8:29:9:82,9,0 1 137825 . G A 1234.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=3.923;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=2.0622;MLEAC=4;MLEAF=0.500;MQ=25.80;MQ0=10;MQRankSum=0.757;QD=9.96;ReadPosRankSum=0.698 GT:AD:DP:GQ:PL 0/1:18,16:34:99:367,0,286 0/1:21,12:33:99:239,0,389 0/1:14,13:27:99:292,0,223 0/1:13,17:30:99:369,0,222 1 138156 . G T 450.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=3.274;DP=117;Dels=0.00;FS=2.297;HaplotypeScore=0.9604;MLEAC=4;MLEAF=0.500;MQ=16.42;MQ0=53;MQRankSum=-0.722;QD=3.85;ReadPosRankSum=-2.151 GT:AD:DP:GQ:PL 0/1:26,8:34:64:64,0,254 0/1:25,13:39:99:222,0,324 0/1:9,7:16:85:85,0,85 0/1:18,9:27:57:112,0,57 1 139058 . C G 422.32 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-0.684;DP=131;Dels=0.00;FS=0.000;HaplotypeScore=0.8025;MLEAC=3;MLEAF=0.375;MQ=39.65;MQ0=17;MQRankSum=-6.454;QD=4.18;ReadPosRankSum=1.712 GT:AD:DP:GQ:PL 0/0:24,6:30:12:0,12,643 0/1:17,10:27:88:88,0,461 0/1:23,13:36:99:224,0,558 0/1:19,19:38:99:144,0,513 1 139781 . G A 153.56 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=13.92;MQ0=7;QD=8.53 GT:AD:DP:GQ:PL ./. 1/1:0,5:5:3:26,3,0 1/1:0,8:8:12:104,12,0 1/1:0,5:5:6:48,6,0 1 139967 . T C 115.39 HARD_TO_VALIDATE AC=5;AF=0.833;AN=6;BaseQRankSum=-0.592;DP=42;Dels=0.00;FS=6.690;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.833;MQ=13.36;MQ0=26;MQRankSum=1.775;QD=3.61;ReadPosRankSum=-2.451 GT:AD:DP:GQ:PL ./. 1/1:6,7:13:3:34,3,0 1/1:2,6:8:6:69,6,0 0/1:3,8:11:14:40,0,14 1 157259 . G A 1029.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.592;DP=111;Dels=0.00;FS=7.876;HaplotypeScore=0.2892;MLEAC=4;MLEAF=0.500;MQ=19.60;MQ0=16;MQRankSum=-0.343;QD=9.28;ReadPosRankSum=0.526 GT:AD:DP:GQ:PL 0/1:14,10:25:99:188,0,182 0/1:15,16:31:99:293,0,217 0/1:14,11:25:99:209,0,179 0/1:12,18:30:99:372,0,113 1 165027 . A G 62.22 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-2.793;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=6.52;MQ0=92;MQRankSum=0.244;QD=0.60;ReadPosRankSum=2.533 GT:AD:DP:GQ:PL 0/1:20,8:28:16:40,0,16 0/1:23,3:26:19:19,0,19 0/1:19,2:21:19:19,0,19 0/1:21,8:29:16:16,0,40 1 167668 . G A 93.43 HARD_TO_VALIDATE;LowQD AC=3;AF=0.500;AN=6;BaseQRankSum=2.843;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=7.32;MQ0=95;MQRankSum=0.000;QD=1.09;ReadPosRankSum=-1.813 GT:AD:DP:GQ:PL ./. 0/1:23,8:31:38:66,0,38 0/1:18,4:22:19:19,0,21 0/1:24,9:33:38:38,0,64 1 167698 . C T 221.47 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=0.713;DP=129;Dels=0.00;FS=0.000;HaplotypeScore=0.2167;MLEAC=5;MLEAF=0.625;MQ=9.13;MQ0=105;MQRankSum=0.651;QD=1.72;ReadPosRankSum=-0.093 GT:AD:DP:GQ:PL 1/1:23,4:27:3:26,3,0 0/1:28,11:39:51:134,0,51 0/1:21,6:28:39:39,0,41 0/1:26,8:35:54:54,0,106 1 167769 . G A 35.37 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=3.712;DP=153;Dels=0.00;FS=0.000;HaplotypeScore=1.0589;MLEAC=3;MLEAF=0.375;MQ=10.78;MQ0=111;MQRankSum=0.641;QD=0.32;ReadPosRankSum=-0.135 GT:AD:DP:GQ:PL 0/1:30,3:33:6:6,0,137 0/1:38,8:46:56:56,0,105 0/1:26,5:31:5:5,0,132 0/0:41,2:43:16:0,16,317 1 172877 . G C 60.28 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.984;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=8.46;MQ0=83;MQRankSum=-2.835;QD=1.44;ReadPosRankSum=-2.025 GT:AD:DP:GQ:PL 0/0:31,3:34:9:0,9,81 1/1:17,4:21:6:55,6,0 0/0:14,8:22:9:0,9,89 0/1:15,6:21:41:41,0,47 1 173098 . C T 429.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=4.288;DP=113;Dels=0.00;FS=0.000;HaplotypeScore=0.4322;MLEAC=4;MLEAF=0.500;MQ=15.11;MQ0=60;MQRankSum=-3.209;QD=3.80;ReadPosRankSum=-0.104 GT:AD:DP:GQ:PL 0/1:15,11:26:89:89,0,92 0/1:23,11:34:99:162,0,106 0/1:17,6:24:47:47,0,222 0/1:14,15:29:82:164,0,82 1 174217 . G A 174.08 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=3.510;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=9.38;MQ0=72;MQRankSum=-0.400;QD=1.93;ReadPosRankSum=-0.133 GT:AD:DP:GQ:PL 0/1:15,4:20:49:80,0,49 0/1:19,6:25:19:19,0,43 0/1:19,2:21:19:39,0,19 0/1:21,3:24:16:68,0,16 1 174302 . G A 57.58 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.383;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=5.93;MQ0=106;MQRankSum=-0.741;QD=0.64;ReadPosRankSum=1.447 GT:AD:DP:GQ:PL 0/0:25,1:26:3:0,3,22 0/1:30,6:36:18:18,0,44 1/1:22,5:27:3:27,3,0 0/1:21,6:27:19:44,0,19 1 227919 . A T 87.26 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=0.742;DP=14;Dels=0.00;FS=6.990;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=16.18;MQ0=7;MQRankSum=0.742;QD=6.23;ReadPosRankSum=-0.742 GT:AD:DP:GQ:PL 1/1:0,3:3:3:34,3,0 1/1:0,3:3:3:30,3,0 1/1:0,2:2:3:30,3,0 0/1:1,5:6:20:21,0,20 1 229673 . A C 453.20 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=19.34;MQ0=19;QD=11.05 GT:AD:DP:GQ:PL 1/1:0,8:8:6:58,6,0 1/1:0,14:14:21:210,21,0 1/1:0,7:7:3:28,3,0 1/1:0,12:12:18:182,18,0 1 229868 . C T 193.97 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.259;DP=128;Dels=0.00;FS=18.115;HaplotypeScore=1.6735;MLEAC=4;MLEAF=0.500;MQ=25.99;MQ0=20;MQRankSum=-0.551;QD=1.52;ReadPosRankSum=-1.793 GT:AD:DP:GQ:PL 0/1:22,4:26:62:62,0,353 0/1:26,8:34:99:104,0,515 0/1:26,6:32:20:20,0,499 0/1:27,9:36:40:40,0,549 1 230047 . A T 657.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.246;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=1.5188;MLEAC=4;MLEAF=0.500;MQ=26.51;MQ0=13;MQRankSum=0.103;QD=5.31;ReadPosRankSum=3.365 GT:AD:DP:GQ:PL 0/1:17,9:26:99:161,0,338 0/1:15,13:28:99:267,0,265 0/1:25,10:35:99:147,0,542 0/1:25,10:35:99:115,0,520 1 230058 . T G 2676.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=0.4247;MLEAC=8;MLEAF=1.00;MQ=25.00;MQ0=18;QD=21.76 GT:AD:DP:GQ:PL 1/1:0,26:26:66:635,66,0 1/1:0,27:27:63:594,63,0 1/1:0,32:32:75:744,75,0 1/1:0,38:38:78:729,78,0 1 231054 . T A 338.90 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-0.386;DP=192;Dels=0.00;FS=1.949;HaplotypeScore=2.4939;MLEAC=3;MLEAF=0.375;MQ=16.76;MQ0=80;MQRankSum=2.301;QD=2.12;ReadPosRankSum=3.705 GT:AD:DP:GQ:PL 0/0:27,5:32:36:0,36,322 0/1:43,10:53:99:136,0,488 0/1:45,11:56:99:135,0,510 0/1:44,7:51:99:102,0,552 1 231070 . A T 143.45 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.698;DP=197;Dels=0.00;FS=24.252;HaplotypeScore=0.4314;MLEAC=3;MLEAF=0.375;MQ=18.20;MQ0=53;MQRankSum=-5.929;QD=1.00;ReadPosRankSum=-3.813 GT:AD:DP:GQ:PL 0/1:19,8:27:36:36,0,257 0/1:42,19:61:99:138,0,722 0/1:45,11:56:1:1,0,753 0/0:42,11:53:28:0,28,789 1 231091 . G C 192.55 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=5.040;DP=192;Dels=0.00;FS=17.031;HaplotypeScore=1.0694;MLEAC=4;MLEAF=0.500;MQ=16.86;MQ0=62;MQRankSum=-5.583;QD=1.44;ReadPosRankSum=1.377 GT:AD:DP:GQ:PL 0/1:16,11:27:51:51,0,135 0/1:40,18:58:99:156,0,552 0/1:36,13:49:16:16,0,613 0/0:45,13:58:1:0,1,525 1 231123 . A G 260.04 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=3.077;DP=221;Dels=0.00;FS=4.823;HaplotypeScore=1.8792;MLEAC=3;MLEAF=0.375;MQ=13.53;MQ0=116;MQRankSum=-4.524;QD=1.71;ReadPosRankSum=2.924 GT:AD:DP:GQ:PL 0/1:33,11:44:54:54,0,111 0/1:41,18:59:99:192,0,271 0/1:35,13:49:46:46,0,368 0/0:57,12:69:4:0,4,559 1 231142 . C G 292.05 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.666;DP=233;Dels=0.00;FS=5.057;HaplotypeScore=0.7727;MLEAC=4;MLEAF=0.500;MQ=11.94;MQ0=146;MQRankSum=-2.375;QD=1.25;ReadPosRankSum=0.608 GT:AD:DP:GQ:PL 0/1:40,8:49:57:57,0,86 0/1:55,13:68:99:195,0,244 0/1:41,10:51:58:58,0,272 0/1:58,7:65:14:14,0,415 1 231175 . T G 625.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.854;DP=314;Dels=0.00;FS=59.302;HaplotypeScore=1.0238;MLEAC=4;MLEAF=0.500;MQ=10.60;MQ0=228;MQRankSum=0.111;QD=1.99;ReadPosRankSum=-0.805 GT:AD:DP:GQ:PL 0/1:55,14:69:35:35,0,85 0/1:64,34:98:99:325,0,281 0/1:41,19:60:99:177,0,181 0/1:70,17:87:99:121,0,295 1 231205 . T A 1267.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.715;DP=388;Dels=0.00;FS=112.989;HaplotypeScore=1.0550;MLEAC=4;MLEAF=0.500;MQ=13.36;MQ0=219;MQRankSum=1.522;QD=3.27;ReadPosRankSum=1.112 GT:AD:DP:GQ:PL 0/1:53,24:79:99:211,0,132 0/1:68,48:116:99:511,0,462 0/1:55,30:85:99:277,0,493 0/1:79,29:108:99:301,0,517 1 231214 . C A 1693.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.490;DP=411;Dels=0.00;FS=134.741;HaplotypeScore=1.6632;MLEAC=4;MLEAF=0.500;MQ=14.14;MQ0=211;MQRankSum=2.065;QD=4.12;ReadPosRankSum=-0.877 GT:AD:DP:GQ:PL 0/1:51,34:85:99:370,0,134 0/1:68,53:121:99:570,0,547 0/1:55,37:92:99:393,0,501 0/1:79,34:113:99:393,0,529 1 231229 . C A 2104.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.248;DP=428;Dels=0.00;FS=158.513;HaplotypeScore=2.4640;MLEAC=4;MLEAF=0.500;MQ=15.15;MQ0=194;MQRankSum=4.874;QD=4.92;ReadPosRankSum=-1.606 GT:AD:DP:GQ:PL 0/1:52,38:90:99:481,0,190 0/1:63,58:121:99:685,0,554 0/1:54,43:97:99:476,0,584 0/1:79,38:118:99:495,0,604 1 231246 . T C 2657.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.163;DP=443;Dels=0.00;FS=180.862;HaplotypeScore=0.8971;MLEAC=4;MLEAF=0.500;MQ=16.32;MQ0=169;MQRankSum=2.022;QD=6.00;ReadPosRankSum=-0.190 GT:AD:DP:GQ:PL 0/1:50,44:94:99:700,0,275 0/1:57,60:117:99:757,0,590 0/1:57,47:104:99:559,0,693 0/1:82,46:128:99:674,0,700 1 231296 . C T 199.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.625;DP=382;Dels=0.00;FS=33.695;HaplotypeScore=2.6855;MLEAC=3;MLEAF=0.375;MQ=17.47;MQ0=127;MQRankSum=1.789;QD=0.71;ReadPosRankSum=1.801 GT:AD:DP:GQ:PL 0/0:92,7:99:50:0,50,1402 0/1:90,12:102:48:48,0,1088 0/1:74,10:84:47:47,0,1002 0/1:83,14:97:99:139,0,1093 1 231480 . G C 731.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-10.527;DP=477;Dels=0.00;FS=6.608;HaplotypeScore=5.1775;MLEAC=4;MLEAF=0.500;MQ=20.20;MQ0=112;MQRankSum=-1.146;QD=1.53;ReadPosRankSum=1.801 GT:AD:DP:GQ:PL 0/1:91,19:110:99:205,0,1325 0/1:104,32:136:99:226,0,1865 0/1:93,19:112:99:122,0,1657 0/1:95,22:117:99:211,0,1504 1 231504 . G A 3721.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=4.992;DP=526;Dels=0.00;FS=1.638;HaplotypeScore=3.6062;MLEAC=4;MLEAF=0.500;MQ=22.19;MQ0=51;MQRankSum=-2.397;QD=7.08;ReadPosRankSum=0.057 GT:AD:DP:GQ:PL 0/1:69,50:119:99:860,0,1198 0/1:85,70:156:99:1190,0,1512 0/1:70,58:128:99:1059,0,1265 0/1:80,43:123:99:645,0,1504 1 231526 . C T 1021.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-4.980;DP=486;Dels=0.00;FS=4.227;HaplotypeScore=3.4683;MLEAC=4;MLEAF=0.500;MQ=22.53;MQ0=55;MQRankSum=-0.401;QD=2.10;ReadPosRankSum=-1.011 GT:AD:DP:GQ:PL 0/1:82,27:110:99:352,0,1655 0/1:116,25:141:99:212,0,2265 0/1:99,22:121:99:197,0,2036 0/1:88,26:114:99:293,0,1864 1 232501 . A T 268.12 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.898;DP=175;Dels=0.01;FS=26.068;HaplotypeScore=0.7664;MLEAC=4;MLEAF=0.500;MQ=25.58;MQ0=48;MQRankSum=-2.777;QD=1.53;ReadPosRankSum=0.818 GT:AD:DP:GQ:PL 0/1:23,7:30:12:12,0,410 0/1:33,14:47:24:24,0,682 0/1:22,26:48:99:122,0,483 0/1:21,27:48:99:142,0,391 1 232648 . C T 121.15 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.151;DP=238;Dels=0.00;FS=10.333;HaplotypeScore=0.2167;MLEAC=3;MLEAF=0.375;MQ=10.03;MQ0=188;MQRankSum=-1.035;QD=0.64;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:42,5:48:15:15,0,102 0/1:61,6:67:41:41,0,277 0/0:41,7:49:18:0,18,177 0/1:65,9:74:99:99,0,211 1 232744 . A G 171.94 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.171;DP=324;Dels=0.00;FS=44.471;HaplotypeScore=2.1574;MLEAC=3;MLEAF=0.375;MQ=20.82;MQ0=117;MQRankSum=-2.401;QD=0.71;ReadPosRankSum=-1.637 GT:AD:DP:GQ:PL 0/1:58,8:66:85:85,0,843 0/0:70,11:81:23:0,23,1147 0/1:71,11:82:68:68,0,906 0/1:81,14:95:53:53,0,1102 1 232752 . G C 92.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.446;DP=317;Dels=0.00;FS=39.427;HaplotypeScore=2.3769;MLEAC=3;MLEAF=0.375;MQ=21.01;MQ0=121;MQRankSum=-2.894;QD=0.39;ReadPosRankSum=-1.224 GT:AD:DP:GQ:PL 0/1:59,5:64:34:34,0,853 0/0:71,9:80:42:0,42,1098 0/1:72,10:82:62:62,0,948 0/1:79,12:91:31:31,0,1076 1 232756 . A G 34.61 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-6.285;DP=312;Dels=0.00;FS=30.832;HaplotypeScore=2.6064;MLEAC=1;MLEAF=0.125;MQ=21.04;MQ0=121;MQRankSum=-2.344;QD=0.44;ReadPosRankSum=-1.149 GT:AD:DP:GQ:PL 0/0:59,4:64:19:0,19,868 0/0:72,7:79:48:0,48,1137 0/1:69,10:79:66:66,0,874 0/0:79,11:90:10:0,10,1084 1 232930 . C G 301.42 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.364;DP=355;Dels=0.00;FS=20.434;HaplotypeScore=4.7651;MLEAC=3;MLEAF=0.375;MQ=21.86;MQ0=107;MQRankSum=-4.614;QD=1.04;ReadPosRankSum=-1.944 GT:AD:DP:GQ:PL 0/1:66,16:83:99:100,0,940 0/1:82,14:96:70:70,0,1414 0/0:53,12:65:11:0,11,994 0/1:89,22:111:99:165,0,1576 1 232955 . G T 461.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.591;DP=357;Dels=0.00;FS=8.542;HaplotypeScore=39.7716;MLEAC=4;MLEAF=0.500;MQ=22.95;MQ0=71;MQRankSum=-5.146;QD=1.29;ReadPosRankSum=1.488 GT:AD:DP:GQ:PL 0/1:67,18:86:99:126,0,1207 0/1:80,18:98:82:82,0,1693 0/1:50,14:64:34:34,0,987 0/1:84,25:109:99:252,0,1601 1 232960 . C A 710.24 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=0.901;DP=358;Dels=0.00;FS=0.570;HaplotypeScore=39.4919;MLEAC=3;MLEAF=0.375;MQ=22.97;MQ0=62;MQRankSum=-0.871;QD=2.60;ReadPosRankSum=-1.935 GT:AD:DP:GQ:PL 0/0:71,14:85:13:0,13,1294 0/1:69,26:95:99:367,0,1362 0/1:51,16:67:99:181,0,893 0/1:83,28:111:99:196,0,1690 1 232961 . T C 386.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-4.141;DP=356;Dels=0.00;FS=8.551;HaplotypeScore=40.0524;MLEAC=4;MLEAF=0.500;MQ=23.02;MQ0=60;MQRankSum=-4.779;QD=1.09;ReadPosRankSum=3.943 GT:AD:DP:GQ:PL 0/1:65,19:84:99:129,0,1176 0/1:78,15:93:70:70,0,1665 0/1:53,14:67:28:28,0,1051 0/1:86,23:109:99:192,0,1706 1 232962 . G A 384.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.068;DP=357;Dels=0.00;FS=7.350;HaplotypeScore=40.5673;MLEAC=4;MLEAF=0.500;MQ=23.05;MQ0=59;MQRankSum=-4.831;QD=1.08;ReadPosRankSum=4.224 GT:AD:DP:GQ:PL 0/1:66,19:85:99:126,0,1201 0/1:79,15:94:70:70,0,1665 0/1:52,14:67:28:28,0,1033 0/1:87,23:111:99:193,0,1698 1 233056 . C G 34.34 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-3.661;DP=266;Dels=0.00;FS=0.000;HaplotypeScore=2.9727;MLEAC=1;MLEAF=0.125;MQ=16.24;MQ0=132;MQRankSum=-3.067;QD=0.56;ReadPosRankSum=1.935 GT:AD:DP:GQ:PL 0/0:59,5:64:78:0,78,742 0/0:57,3:60:49:0,49,692 0/1:52,9:61:66:66,0,430 0/0:75,4:79:51:0,51,938 1 233086 . G A 1298.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.855;DP=245;Dels=0.00;FS=9.376;HaplotypeScore=1.2269;MLEAC=4;MLEAF=0.500;MQ=17.57;MQ0=128;MQRankSum=-0.955;QD=5.30;ReadPosRankSum=1.386 GT:AD:DP:GQ:PL 0/1:33,25:58:99:236,0,285 0/1:34,31:65:99:440,0,281 0/1:28,23:51:99:236,0,266 0/1:43,28:71:99:419,0,395 1 233913 . A G 60.21 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.350;DP=256;Dels=0.00;FS=5.563;HaplotypeScore=0.4079;MLEAC=3;MLEAF=0.375;MQ=6.52;MQ0=232;MQRankSum=-0.953;QD=0.31;ReadPosRankSum=1.334 GT:AD:DP:GQ:PL 0/0:53,10:63:9:0,9,82 0/1:49,9:58:12:12,0,104 0/1:55,13:68:12:12,0,97 0/1:56,10:66:38:69,0,38 1 234378 . A G 611.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-9.587;DP=396;Dels=0.00;FS=7.812;HaplotypeScore=2.5533;MLEAC=4;MLEAF=0.500;MQ=30.27;MQ0=73;MQRankSum=-3.938;QD=1.55;ReadPosRankSum=1.196 GT:AD:DP:GQ:PL 0/1:75,29:104:99:183,0,1613 0/1:88,24:112:99:185,0,2096 0/1:68,23:91:99:116,0,1455 0/1:64,23:87:99:160,0,1343 1 234432 . A G 215.90 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-7.042;DP=317;Dels=0.00;FS=46.402;HaplotypeScore=2.4109;MLEAC=3;MLEAF=0.375;MQ=33.26;MQ0=24;MQRankSum=-3.723;QD=0.88;ReadPosRankSum=-3.365 GT:AD:DP:GQ:PL 0/1:64,18:83:74:74,0,1580 0/1:59,15:74:61:61,0,1535 0/0:58,13:71:76:0,76,1557 0/1:67,22:89:99:115,0,1649 1 234466 . C T 409.91 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=1.584;DP=317;Dels=0.00;FS=18.056;HaplotypeScore=2.6981;MLEAC=3;MLEAF=0.375;MQ=31.23;MQ0=44;MQRankSum=-3.368;QD=1.82;ReadPosRankSum=2.504 GT:AD:DP:GQ:PL 0/1:64,12:76:99:165,0,1334 0/1:73,11:84:94:94,0,1476 0/1:52,13:65:99:185,0,967 0/0:80,12:92:30:0,30,1676 1 234481 . T A 1828.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.618;DP=317;Dels=0.00;FS=58.108;HaplotypeScore=3.3352;MLEAC=4;MLEAF=0.500;MQ=30.16;MQ0=65;MQRankSum=-3.407;QD=5.77;ReadPosRankSum=3.442 GT:AD:DP:GQ:PL 0/1:42,34:76:99:494,0,895 0/1:42,36:80:99:515,0,864 0/1:40,24:64:99:164,0,855 0/1:52,45:97:99:688,0,797 1 234575 . C T 37.33 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=0.338;DP=329;Dels=0.00;FS=49.010;HaplotypeScore=0.9948;MLEAC=1;MLEAF=0.125;MQ=24.28;MQ0=91;MQRankSum=-4.898;QD=0.42;ReadPosRankSum=0.887 GT:AD:DP:GQ:PL 0/0:63,6:69:90:0,90,1411 0/0:64,8:72:73:0,73,1494 0/1:71,16:88:69:69,0,1258 0/0:90,9:99:40:0,40,1552 1 234609 . T C 333.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.263;DP=369;Dels=0.00;FS=9.060;HaplotypeScore=4.5467;MLEAC=3;MLEAF=0.375;MQ=25.88;MQ0=84;MQRankSum=2.126;QD=1.21;ReadPosRankSum=0.265 GT:AD:DP:GQ:PL 0/1:63,10:74:99:117,0,1118 0/1:83,13:96:91:91,0,1749 0/0:86,5:92:47:0,47,1584 0/1:91,15:106:99:160,0,1700 1 234760 . A T 314.91 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-2.557;DP=204;Dels=0.00;FS=61.961;HaplotypeScore=3.0355;MLEAC=3;MLEAF=0.375;MQ=26.69;MQ0=39;MQRankSum=-3.605;QD=1.89;ReadPosRankSum=-3.067 GT:AD:DP:GQ:PL 0/0:25,11:37:34:0,34,668 0/1:35,19:54:99:115,0,927 0/1:24,25:49:99:191,0,582 0/1:45,18:63:43:43,0,1136 1 235012 . G A 555.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=5.825;DP=274;Dels=0.00;FS=19.891;HaplotypeScore=0.2080;MLEAC=4;MLEAF=0.500;MQ=14.94;MQ0=166;MQRankSum=1.089;QD=2.03;ReadPosRankSum=-1.238 GT:AD:DP:GQ:PL 0/1:57,13:70:99:164,0,336 0/1:73,13:86:99:134,0,611 0/1:38,9:47:87:87,0,272 0/1:57,14:71:99:203,0,282 1 235844 . C G 2245.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=5.452;DP=395;Dels=0.00;FS=3.548;HaplotypeScore=2.5349;MLEAC=4;MLEAF=0.500;MQ=19.25;MQ0=181;MQRankSum=1.141;QD=5.69;ReadPosRankSum=-2.814 GT:AD:DP:GQ:PL 0/1:67,35:104:99:753,0,686 0/1:63,30:93:99:519,0,476 0/1:67,23:90:99:345,0,724 0/1:64,43:107:99:661,0,494 1 235929 . G A 837.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=6.671;DP=220;Dels=0.00;FS=49.873;HaplotypeScore=1.1223;MLEAC=4;MLEAF=0.500;MQ=31.15;MQ0=27;MQRankSum=-9.545;QD=3.81;ReadPosRankSum=-0.147 GT:AD:DP:GQ:PL 0/1:33,18:51:99:102,0,846 0/1:38,26:64:99:254,0,911 0/1:28,22:50:99:241,0,686 0/1:30,25:55:99:273,0,743 1 235976 . C A 3069.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.045;DP=271;Dels=0.00;FS=3.956;HaplotypeScore=2.1549;MLEAC=4;MLEAF=0.500;MQ=28.73;MQ0=46;MQRankSum=8.503;QD=11.33;ReadPosRankSum=1.000 GT:AD:DP:GQ:PL 0/1:32,34:66:99:908,0,361 0/1:41,27:68:99:625,0,597 0/1:34,21:55:99:558,0,475 0/1:43,39:82:99:1011,0,607 1 236793 . T C 142.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.712;DP=316;Dels=0.00;FS=0.000;HaplotypeScore=0.2367;MLEAC=4;MLEAF=0.500;MQ=8.10;MQ0=273;MQRankSum=-0.821;QD=0.45;ReadPosRankSum=-0.654 GT:AD:DP:GQ:PL 0/1:68,12:80:40:40,0,60 0/1:78,10:89:32:32,0,312 0/1:54,9:63:76:76,0,157 0/1:79,5:84:27:27,0,143 1 236848 . T C 221.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-3.438;DP=317;Dels=0.00;FS=0.000;HaplotypeScore=1.3662;MLEAC=4;MLEAF=0.500;MQ=10.45;MQ0=244;MQRankSum=0.132;QD=0.70;ReadPosRankSum=2.181 GT:AD:DP:GQ:PL 0/1:66,9:75:49:49,0,174 0/1:80,10:90:93:93,0,394 0/1:57,8:65:82:82,0,296 0/1:75,12:87:30:30,0,302 1 237272 . T A 547.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.596;DP=299;Dels=0.00;FS=0.000;HaplotypeScore=3.2050;MLEAC=4;MLEAF=0.500;MQ=22.45;MQ0=43;MQRankSum=-1.986;QD=1.83;ReadPosRankSum=0.229 GT:AD:DP:GQ:PL 0/1:54,11:65:99:148,0,998 0/1:65,16:81:99:217,0,1120 0/1:59,12:71:99:111,0,1294 0/1:69,12:81:99:104,0,1148 1 237448 . T G 166.91 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.257;DP=226;Dels=0.00;FS=4.521;HaplotypeScore=3.5900;MLEAC=4;MLEAF=0.500;MQ=18.70;MQ0=96;MQRankSum=-2.139;QD=0.74;ReadPosRankSum=-0.424 GT:AD:DP:GQ:PL 0/1:38,3:45:4:4,0,404 0/1:48,7:61:43:43,0,630 0/1:42,6:54:76:76,0,635 0/1:48,8:66:75:75,0,621 1 237490 . C A 382.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.238;DP=201;Dels=0.00;FS=0.821;HaplotypeScore=5.2048;MLEAC=4;MLEAF=0.500;MQ=22.57;MQ0=54;MQRankSum=-1.240;QD=1.91;ReadPosRankSum=0.233 GT:AD:DP:GQ:PL 0/1:35,6:41:52:52,0,565 0/1:50,11:61:95:95,0,697 0/1:44,7:52:99:124,0,596 0/1:36,10:47:99:144,0,570 1 237505 . T C 179.92 HARD_TO_VALIDATE AC=2;AF=0.250;AN=8;BaseQRankSum=-3.018;DP=199;Dels=0.00;FS=0.000;HaplotypeScore=3.8204;MLEAC=2;MLEAF=0.250;MQ=23.45;MQ0=50;MQRankSum=1.582;QD=2.04;ReadPosRankSum=-0.505 GT:AD:DP:GQ:PL 0/1:29,7:36:98:98,0,447 0/0:50,4:55:25:0,25,720 0/1:40,10:52:99:116,0,596 0/0:50,5:56:58:0,58,975 1 237752 . A G 234.97 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.439;DP=203;Dels=0.00;FS=92.481;HaplotypeScore=2.9828;MLEAC=4;MLEAF=0.500;MQ=27.44;MQ0=21;MQRankSum=-3.539;QD=1.16;ReadPosRankSum=-1.453 GT:AD:DP:GQ:PL 0/1:30,9:39:97:97,0,667 0/1:44,13:57:68:68,0,1015 0/1:42,16:58:82:82,0,933 0/1:42,7:49:20:20,0,889 1 237794 . C T 326.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=5.187;DP=295;Dels=0.00;FS=40.713;HaplotypeScore=1.9875;MLEAC=3;MLEAF=0.375;MQ=29.74;MQ0=48;MQRankSum=-0.013;QD=1.48;ReadPosRankSum=-0.633 GT:AD:DP:GQ:PL 0/1:49,8:57:99:119,0,852 0/0:71,3:74:95:0,95,1369 0/1:67,8:75:89:89,0,1103 0/1:79,10:89:99:153,0,1353 1 237805 . A G 534.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.015;DP=300;Dels=0.00;FS=0.000;HaplotypeScore=2.5458;MLEAC=4;MLEAF=0.500;MQ=29.26;MQ0=45;MQRankSum=-3.184;QD=1.78;ReadPosRankSum=-2.425 GT:AD:DP:GQ:PL 0/1:43,12:57:99:137,0,852 0/1:63,14:77:49:49,0,1328 0/1:61,15:76:86:86,0,1277 0/1:67,23:90:99:295,0,1438 1 237881 . G T 405.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.130;DP=237;Dels=0.00;FS=50.608;HaplotypeScore=3.3633;MLEAC=4;MLEAF=0.500;MQ=28.65;MQ0=44;MQRankSum=-2.356;QD=1.71;ReadPosRankSum=-6.076 GT:AD:DP:GQ:PL 0/1:33,16:49:54:54,0,807 0/1:37,21:59:70:70,0,919 0/1:38,25:63:99:169,0,1005 0/1:46,20:66:99:145,0,1074 1 238216 . A C 86.96 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.403;DP=234;Dels=0.00;FS=0.825;HaplotypeScore=2.3781;MLEAC=2;MLEAF=0.250;MQ=21.26;MQ0=51;MQRankSum=-3.446;QD=0.74;ReadPosRankSum=-2.197 GT:AD:DP:GQ:PL 0/0:52,6:58:35:0,35,1135 0/1:47,9:56:84:84,0,739 0/0:49,9:58:19:0,19,996 0/1:49,13:62:37:37,0,1017 1 238267 . C T 910.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.839;DP=194;Dels=0.00;FS=0.000;HaplotypeScore=1.5836;MLEAC=4;MLEAF=0.500;MQ=25.70;MQ0=39;MQRankSum=-5.122;QD=4.70;ReadPosRankSum=-1.545 GT:AD:DP:GQ:PL 0/1:27,20:47:99:236,0,609 0/1:32,16:48:99:140,0,783 0/1:27,23:50:99:216,0,620 0/1:26,23:49:99:351,0,508 1 239164 . G A 59.20 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.648;DP=129;Dels=0.00;FS=1.859;HaplotypeScore=0.6938;MLEAC=3;MLEAF=0.375;MQ=12.62;MQ0=89;MQRankSum=-1.943;QD=0.55;ReadPosRankSum=-0.551 GT:AD:DP:GQ:PL 0/0:20,0:21:15:0,15,145 0/1:31,8:39:18:18,0,245 0/1:20,7:28:24:24,0,168 0/1:31,10:41:51:51,0,174 1 239532 . C T 428.73 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.152;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=1.1146;MLEAC=4;MLEAF=0.500;MQ=12.38;MQ0=73;MQRankSum=0.992;QD=4.01;ReadPosRankSum=-0.430 GT:AD:DP:GQ:PL 0/1:12,7:19:5:121,0,5 0/1:17,11:28:53:134,0,53 0/1:17,12:29:88:91,0,88 0/1:16,15:31:60:114,0,60 1 240147 . C T 108.39 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.862;DP=155;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=12.19;MQ0=111;MQRankSum=-0.602;QD=0.70;ReadPosRankSum=1.078 GT:AD:DP:GQ:PL 0/1:33,5:38:36:36,0,117 0/1:38,11:49:39:39,0,319 0/1:18,4:22:62:62,0,119 0/1:42,4:46:2:2,0,199 1 240853 . G A 57.95 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.671;DP=166;Dels=0.00;FS=8.789;HaplotypeScore=0.6714;MLEAC=2;MLEAF=0.250;MQ=23.03;MQ0=46;MQRankSum=-3.663;QD=0.75;ReadPosRankSum=0.382 GT:AD:DP:GQ:PL 0/1:29,5:34:39:39,0,536 0/0:45,7:52:20:0,20,783 0/0:34,3:37:66:0,66,660 0/1:31,12:43:53:53,0,499 1 240898 . T G 237.93 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-6.776;DP=153;Dels=0.00;FS=15.219;HaplotypeScore=0.7169;MLEAC=3;MLEAF=0.375;MQ=19.27;MQ0=65;MQRankSum=-3.215;QD=1.86;ReadPosRankSum=2.075 GT:AD:DP:GQ:PL 0/1:27,13:40:99:139,0,397 0/1:41,12:53:44:44,0,524 0/0:21,4:25:24:0,24,239 0/1:26,9:35:89:89,0,273 1 241263 . C T 123.91 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=5.364;DP=160;Dels=0.00;FS=11.735;HaplotypeScore=3.0928;MLEAC=3;MLEAF=0.375;MQ=29.30;MQ0=6;MQRankSum=-1.004;QD=1.08;ReadPosRankSum=-1.950 GT:AD:DP:GQ:PL 0/1:21,3:24:34:34,0,357 0/0:40,5:45:37:0,37,962 0/1:46,5:51:28:28,0,932 0/1:32,8:40:96:96,0,650 1 241369 . C T 1204.39 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=1.5471;MLEAC=8;MLEAF=1.00;MQ=26.78;MQ0=16;QD=18.25 GT:AD:DP:GQ:PL 1/1:0,12:12:15:160,15,0 1/1:0,13:13:24:235,24,0 1/1:0,15:15:33:340,33,0 1/1:0,25:25:48:495,48,0 1 242426 . G A 191.05 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.330;DP=148;Dels=0.00;FS=11.247;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=11.21;MQ0=113;MQRankSum=-0.678;QD=1.29;ReadPosRankSum=-1.338 GT:AD:DP:GQ:PL 0/1:30,7:37:66:95,0,66 0/1:25,5:30:14:14,0,212 0/1:32,11:43:54:54,0,140 0/1:32,6:38:60:60,0,115 1 243396 . A G 147.70 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-6.752;DP=199;Dels=0.00;FS=0.000;HaplotypeScore=1.0286;MLEAC=3;MLEAF=0.375;MQ=16.06;MQ0=78;MQRankSum=-0.003;QD=0.98;ReadPosRankSum=-0.241 GT:AD:DP:GQ:PL 0/0:43,5:49:9:0,9,554 0/1:45,10:55:86:86,0,498 0/1:39,10:49:45:45,0,501 0/1:38,8:46:50:50,0,428 1 244272 . T A 74.33 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.779;DP=186;Dels=0.00;FS=2.650;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=15.47;MQ0=102;MQRankSum=0.655;QD=0.40;ReadPosRankSum=0.866 GT:AD:DP:GQ:PL 0/1:40,10:50:25:25,0,427 0/1:44,13:57:65:65,0,519 0/1:32,6:38:3:3,0,372 0/1:39,2:41:12:12,0,314 1 244288 . A G 339.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-4.014;DP=151;Dels=0.00;FS=0.000;HaplotypeScore=0.2416;MLEAC=4;MLEAF=0.500;MQ=14.20;MQ0=93;MQRankSum=-0.361;QD=2.25;ReadPosRankSum=0.393 GT:AD:DP:GQ:PL 0/1:24,15:39:99:109,0,136 0/1:31,20:51:99:160,0,308 0/1:22,8:30:74:74,0,193 0/1:25,6:31:29:29,0,160 1 245268 . T A 142.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.116;DP=141;Dels=0.00;FS=4.630;HaplotypeScore=2.7232;MLEAC=3;MLEAF=0.375;MQ=20.53;MQ0=32;MQRankSum=-3.389;QD=1.35;ReadPosRankSum=-0.858 GT:AD:DP:GQ:PL 0/1:27,5:32:55:55,0,374 0/0:32,3:35:28:0,28,613 0/1:30,9:39:74:74,0,534 0/1:29,6:35:48:48,0,540 1 245328 . A G 304.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-4.120;DP=113;Dels=0.00;FS=10.151;HaplotypeScore=17.4569;MLEAC=4;MLEAF=0.500;MQ=21.99;MQ0=22;MQRankSum=-2.860;QD=2.70;ReadPosRankSum=-0.869 GT:AD:DP:GQ:PL 0/1:15,6:21:90:90,0,112 0/1:23,5:28:49:49,0,360 0/1:28,8:36:80:80,0,525 0/1:21,7:28:99:118,0,375 1 245894 . G A 129.35 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=4.488;DP=181;Dels=0.00;FS=2.602;HaplotypeScore=1.3879;MLEAC=3;MLEAF=0.375;MQ=10.32;MQ0=127;MQRankSum=-1.993;QD=0.92;ReadPosRankSum=1.378 GT:AD:DP:GQ:PL 0/1:34,9:43:68:68,0,162 0/1:36,6:42:21:21,0,163 0/0:33,8:41:12:0,12,109 0/1:41,14:55:74:74,0,151 1 246977 . A C 261.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.761;DP=229;Dels=0.00;FS=0.000;HaplotypeScore=0.1663;MLEAC=4;MLEAF=0.500;MQ=10.49;MQ0=164;MQRankSum=-1.935;QD=1.14;ReadPosRankSum=-0.047 GT:AD:DP:GQ:PL 0/1:40,18:58:99:140,0,240 0/1:40,15:55:44:44,0,162 0/1:37,14:51:53:53,0,78 0/1:43,22:65:57:57,0,211 1 247428 . G T 1041.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.738;DP=191;Dels=0.00;FS=1.438;HaplotypeScore=1.8617;MLEAC=4;MLEAF=0.500;MQ=22.23;MQ0=42;MQRankSum=0.458;QD=5.46;ReadPosRankSum=0.097 GT:AD:DP:GQ:PL 0/1:26,12:39:99:164,0,392 0/1:21,15:36:99:159,0,361 0/1:36,21:58:99:377,0,581 0/1:30,28:58:99:374,0,455 1 247585 . G A 361 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.794;DP=177;Dels=0.00;FS=63.132;HaplotypeScore=3.2009;MLEAC=4;MLEAF=0.500;MQ=23.32;MQ0=50;MQRankSum=-2.882;QD=2.04;ReadPosRankSum=-1.148 GT:AD:DP:GQ:PL 0/1:21,2:23:17:17,0,275 0/1:30,14:44:99:171,0,474 0/1:40,13:53:99:155,0,607 0/1:46,11:57:50:50,0,821 1 248705 . G T 282.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.986;DP=199;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=11.65;MQ0=136;MQRankSum=-0.258;QD=1.42;ReadPosRankSum=-0.450 GT:AD:DP:GQ:PL 0/1:29,13:42:30:30,0,132 0/1:50,10:60:53:53,0,291 0/1:36,15:51:99:178,0,154 0/1:40,6:46:54:54,0,262 1 249558 . C T 54.49 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=3.826;DP=129;Dels=0.00;FS=68.386;HaplotypeScore=1.1506;MLEAC=2;MLEAF=0.250;MQ=19.26;MQ0=46;MQRankSum=-3.840;QD=0.80;ReadPosRankSum=-3.015 GT:AD:DP:GQ:PL 0/0:14,5:19:30:0,30,285 0/0:38,4:42:29:0,29,611 0/1:23,5:28:6:6,0,312 0/1:29,11:40:81:81,0,379 1 249702 . G A 410.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.528;DP=181;Dels=0.00;FS=0.884;HaplotypeScore=2.6293;MLEAC=4;MLEAF=0.500;MQ=23.73;MQ0=37;MQRankSum=-5.972;QD=2.27;ReadPosRankSum=-1.403 GT:AD:DP:GQ:PL 0/1:29,17:46:99:128,0,573 0/1:25,15:40:99:137,0,465 0/1:33,11:44:94:94,0,682 0/1:37,14:51:84:84,0,726 1 253129 . G C 401.07 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=1.234;DP=201;Dels=0.00;FS=25.347;HaplotypeScore=0.7048;MLEAC=3;MLEAF=0.375;MQ=21.05;MQ0=84;MQRankSum=-0.483;QD=2.67;ReadPosRankSum=2.124 GT:AD:DP:GQ:PL 0/1:43,6:50:93:93,0,408 0/1:32,13:45:99:196,0,380 0/0:47,4:51:16:0,16,644 0/1:42,13:55:99:146,0,642 1 253779 . C A 131.38 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.197;DP=176;Dels=0.00;FS=0.000;HaplotypeScore=0.6999;MLEAC=3;MLEAF=0.375;MQ=9.64;MQ0=148;MQRankSum=0.590;QD=0.93;ReadPosRankSum=0.787 GT:AD:DP:GQ:PL 0/0:26,9:35:6:0,6,59 0/1:36,9:45:29:29,0,207 0/1:35,10:45:44:44,0,74 0/1:43,8:51:91:91,0,120 1 255633 . A G 708.51 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=14.86;MQ0=26;QD=9.08 GT:AD:DP:GQ:PL 1/1:0,19:19:18:176,18,0 1/1:0,20:21:27:252,27,0 1/1:0,18:18:9:80,9,0 1/1:0,20:20:24:226,24,0 1 256498 . A G 1206.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.700;DP=245;Dels=0.00;FS=0.000;HaplotypeScore=2.2717;MLEAC=4;MLEAF=0.500;MQ=23.92;MQ0=11;MQRankSum=0.260;QD=4.93;ReadPosRankSum=0.736 GT:AD:DP:GQ:PL 0/1:40,12:52:99:133,0,873 0/1:44,17:61:99:268,0,975 0/1:39,17:56:99:315,0,863 0/1:45,30:75:99:523,0,920 1 256736 . C T 685.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=7.325;DP=218;Dels=0.00;FS=0.000;HaplotypeScore=2.0460;MLEAC=4;MLEAF=0.500;MQ=19.47;MQ0=89;MQRankSum=0.305;QD=3.15;ReadPosRankSum=0.507 GT:AD:DP:GQ:PL 0/1:37,6:43:64:64,0,375 0/1:37,14:51:99:179,0,538 0/1:40,11:51:99:117,0,488 0/1:52,21:73:99:358,0,542 1 256922 . T A 636.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.161;DP=209;Dels=0.00;FS=17.678;HaplotypeScore=0.3943;MLEAC=4;MLEAF=0.500;MQ=16.82;MQ0=132;MQRankSum=-0.982;QD=3.05;ReadPosRankSum=0.774 GT:AD:DP:GQ:PL 0/1:34,13:47:99:221,0,104 0/1:49,14:63:99:144,0,359 0/1:29,11:40:93:155,0,93 0/1:50,9:59:99:149,0,476 1 257686 . A G 223.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.119;DP=142;Dels=0.00;FS=20.896;HaplotypeScore=0.6596;MLEAC=4;MLEAF=0.500;MQ=17.69;MQ0=99;MQRankSum=0.463;QD=1.58;ReadPosRankSum=-0.198 GT:AD:DP:GQ:PL 0/1:25,6:31:33:33,0,193 0/1:23,9:32:87:87,0,164 0/1:27,9:36:82:82,0,131 0/1:33,10:43:54:54,0,275 1 257881 . T C 360.33 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=1.714;DP=198;Dels=0.00;FS=5.610;HaplotypeScore=1.2720;MLEAC=3;MLEAF=0.375;MQ=18.40;MQ0=76;MQRankSum=-0.771;QD=2.52;ReadPosRankSum=0.333 GT:AD:DP:GQ:PL 0/1:35,6:41:10:10,0,363 0/0:49,6:55:29:0,29,641 0/1:38,12:50:99:133,0,455 0/1:34,17:52:99:251,0,443 1 258930 . C T 915.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=0.6905;MLEAC=8;MLEAF=1.00;MQ=12.68;MQ0=42;QD=9.06 GT:AD:DP:GQ:PL 1/1:0,18:18:24:187,24,0 1/1:0,26:26:36:283,36,0 1/1:0,32:32:30:237,30,0 1/1:0,23:23:30:234,30,0 1 356416 . G A 73.22 HARD_TO_VALIDATE AC=2;AF=0.333;AN=6;BaseQRankSum=1.369;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.2447;MLEAC=2;MLEAF=0.333;MQ=11.03;MQ0=21;MQRankSum=0.660;QD=2.93;ReadPosRankSum=-1.200 GT:AD:DP:GQ:PL 0/1:9,2:11:16:40,0,16 0/1:8,6:14:13:62,0,13 ./. 0/0:5,0:5:3:0,3,25 1 364272 . C A 78.99 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.679;DP=93;Dels=0.00;FS=13.084;HaplotypeScore=0.4547;MLEAC=3;MLEAF=0.375;MQ=12.20;MQ0=63;MQRankSum=-1.539;QD=1.10;ReadPosRankSum=-1.493 GT:AD:DP:GQ:PL 0/1:19,2:21:19:19,0,46 0/0:16,5:21:27:0,27,244 0/1:17,7:24:19:46,0,19 0/1:23,4:27:48:48,0,191 1 364378 . T G 84.33 HARD_TO_VALIDATE;LowQD AC=6;AF=1.00;AN=6;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=5.01;MQ0=75;QD=1.22 GT:AD:DP:GQ:PL ./. 1/1:15,8:23:3:27,3,0 1/1:12,5:17:3:28,3,0 1/1:23,6:29:6:53,6,0 1 384435 . C G 51.32 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.113;DP=222;Dels=0.00;FS=0.000;HaplotypeScore=1.5197;MLEAC=2;MLEAF=0.250;MQ=7.33;MQ0=185;MQRankSum=-0.283;QD=0.44;ReadPosRankSum=1.491 GT:AD:DP:GQ:PL 0/1:58,11:69:16:70,0,16 0/1:43,5:48:13:13,0,85 0/0:51,0:51:12:0,12,112 0/0:46,8:54:3:0,3,43 1 384512 . C G 44.07 HARD_TO_VALIDATE;LowQD;LowQual AC=4;AF=0.500;AN=8;BaseQRankSum=2.259;DP=330;Dels=0.00;FS=0.000;HaplotypeScore=0.1663;MLEAC=4;MLEAF=0.500;MQ=5.91;MQ0=274;MQRankSum=1.189;QD=0.17;ReadPosRankSum=-0.775 GT:AD:DP:GQ:PL 0/1:84,9:97:10:10,0,119 0/1:82,5:88:13:13,0,91 0/0:63,6:69:12:0,12,117 1/1:71,5:76:6:56,6,0 1 404409 . T G 57.51 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=0.998;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.1446;MLEAC=2;MLEAF=0.250;MQ=16.51;MQ0=31;MQRankSum=-1.418;QD=2.30;ReadPosRankSum=-0.788 GT:AD:DP:GQ:PL 0/0:10,1:11:6:0,6,53 0/0:9,2:11:9:0,9,103 0/1:7,2:9:27:57,0,27 1/1:12,4:16:3:34,3,0 1 404428 . C T 34.02 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.500;AN=6;BaseQRankSum=-0.387;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9048;MLEAC=2;MLEAF=0.333;MQ=16.72;MQ0=25;MQRankSum=-1.532;QD=1.48;ReadPosRankSum=1.932 GT:AD:DP:GQ:PL ./. 0/0:9,1:10:9:0,9,98 0/1:7,1:8:31:31,0,31 1/1:9,6:15:3:34,3,0 1 404664 . G T 173.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.107;DP=117;Dels=0.02;FS=13.776;HaplotypeScore=4.9500;MLEAC=4;MLEAF=0.500;MQ=20.37;MQ0=52;MQRankSum=0.959;QD=1.49;ReadPosRankSum=-0.779 GT:AD:DP:GQ:PL 0/1:23,2:25:43:43,0,111 0/1:34,2:36:35:35,0,265 0/1:25,4:29:46:46,0,180 0/1:20,5:25:52:82,0,52 1 404672 . G A 144 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-2.370;DP=110;Dels=0.00;FS=10.788;HaplotypeScore=2.2250;MLEAC=4;MLEAF=0.500;MQ=21.01;MQ0=45;MQRankSum=0.959;QD=1.31;ReadPosRankSum=-0.861 GT:AD:DP:GQ:PL 0/1:23,3:26:17:17,0,113 0/1:32,2:34:34:34,0,258 0/1:22,4:26:40:40,0,176 0/1:19,5:24:51:85,0,51 1 404734 . A G 41.79 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-1.016;DP=93;Dels=0.00;FS=0.000;HaplotypeScore=0.8895;MLEAC=2;MLEAF=0.250;MQ=16.18;MQ0=61;MQRankSum=-0.113;QD=0.87;ReadPosRankSum=-0.384 GT:AD:DP:GQ:PL 0/0:18,2:20:9:0,9,93 0/1:23,2:25:19:19,0,119 0/1:20,3:23:47:56,0,47 0/0:22,2:24:12:0,12,132 1 404971 . T C 56.82 HARD_TO_VALIDATE AC=3;AF=0.500;AN=6;BaseQRankSum=-0.731;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.4663;MLEAC=3;MLEAF=0.500;MQ=15.08;MQ0=28;MQRankSum=-2.166;QD=2.58;ReadPosRankSum=-0.296 GT:AD:DP:GQ:PL ./. 1/1:11,3:14:3:33,3,0 0/0:9,2:11:6:0,6,69 0/1:5,3:8:23:54,0,23 1 404974 . A G 55.82 HARD_TO_VALIDATE AC=3;AF=0.500;AN=6;BaseQRankSum=-1.133;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.4663;MLEAC=3;MLEAF=0.500;MQ=14.90;MQ0=28;MQRankSum=0.000;QD=2.33;ReadPosRankSum=1.568 GT:AD:DP:GQ:PL ./. 1/1:12,2:14:3:33,3,0 0/0:8,1:9:6:0,6,68 0/1:8,2:10:24:53,0,24 1 449336 . C T 62.68 HARD_TO_VALIDATE;LowQD AC=3;AF=0.750;AN=4;BaseQRankSum=-1.380;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=0.3943;MLEAC=3;MLEAF=0.750;MQ=5.00;MQ0=114;MQRankSum=0.720;QD=0.99;ReadPosRankSum=0.720 GT:AD:DP:GQ:PL 0/1:36,2:39:19:19,0,21 ./. ./. 1/1:17,7:24:6:71,6,0 1 521603 . G A 183.58 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=7.037;DP=172;Dels=0.00;FS=2.753;HaplotypeScore=0.7947;MLEAC=3;MLEAF=0.375;MQ=23.01;MQ0=17;MQRankSum=-4.164;QD=1.58;ReadPosRankSum=-0.180 GT:AD:DP:GQ:PL 0/1:28,9:37:83:83,0,425 0/0:50,6:56:10:0,10,980 0/1:35,6:41:21:21,0,760 0/1:29,9:38:99:113,0,533 1 523471 . T C 133.54 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.2167;MLEAC=6;MLEAF=0.750;MQ=14.54;MQ0=14;QD=4.95 GT:AD:DP:GQ:PL 1/1:0,3:3:6:52,6,0 1/1:0,8:9:3:29,3,0 1/1:0,10:10:9:76,9,0 1/1:0,5:5:3:27,3,0 1 523825 . C T 268.16 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=5.314;DP=198;Dels=0.00;FS=0.760;HaplotypeScore=2.1034;MLEAC=4;MLEAF=0.500;MQ=20.50;MQ0=30;MQRankSum=1.049;QD=1.35;ReadPosRankSum=0.361 GT:AD:DP:GQ:PL 0/1:41,10:51:95:95,0,594 0/1:34,6:40:11:11,0,684 0/1:43,13:57:99:166,0,751 0/1:42,7:50:28:28,0,683 1 523948 . C T 84.07 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=0.134;DP=146;Dels=0.00;FS=18.761;HaplotypeScore=0.9295;MLEAC=2;MLEAF=0.250;MQ=12.42;MQ0=101;MQRankSum=-1.024;QD=1.20;ReadPosRankSum=0.638 GT:AD:DP:GQ:PL 0/0:34,2:36:14:0,14,333 0/0:36,4:40:6:0,6,256 0/1:26,4:30:42:42,0,44 0/1:33,7:40:75:75,0,164 1 526057 . T C 747.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-4.094;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=0.9548;MLEAC=4;MLEAF=0.500;MQ=46.12;MQ0=11;MQRankSum=0.965;QD=8.40;ReadPosRankSum=-1.165 GT:AD:DP:GQ:PL 0/1:13,12:25:99:204,0,122 0/1:10,11:21:99:237,0,210 0/1:9,4:13:63:63,0,169 0/1:15,14:29:99:276,0,267 1 533197 . A G 33.02 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=-0.078;DP=157;Dels=0.00;FS=20.720;HaplotypeScore=2.7253;MLEAC=3;MLEAF=0.375;MQ=35.46;MQ0=42;MQRankSum=-0.987;QD=0.27;ReadPosRankSum=-3.060 GT:AD:DP:GQ:PL 0/1:38,4:43:28:28,0,502 0/1:32,2:34:21:21,0,371 0/0:34,0:34:75:0,75,776 0/1:40,6:46:18:18,0,635 1 533300 . G A 187.16 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.845;DP=253;Dels=0.00;FS=0.000;HaplotypeScore=0.9487;MLEAC=4;MLEAF=0.500;MQ=13.28;MQ0=190;MQRankSum=0.297;QD=0.74;ReadPosRankSum=-1.945 GT:AD:DP:GQ:PL 0/1:67,2:69:12:12,0,177 0/1:65,7:72:84:84,0,247 0/1:44,4:48:18:18,0,105 0/1:59,5:64:99:105,0,145 1 533958 . G A 255.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=5.297;DP=487;Dels=0.00;FS=0.000;HaplotypeScore=0.5809;MLEAC=4;MLEAF=0.500;MQ=8.11;MQ0=420;MQRankSum=2.058;QD=0.53;ReadPosRankSum=-2.511 GT:AD:DP:GQ:PL 0/1:95,7:103:55:55,0,71 0/1:141,12:153:86:86,0,159 0/1:117,11:129:35:76,0,35 0/1:96,5:102:71:71,0,175 1 534005 . G A 903.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=7.924;DP=488;Dels=0.00;FS=0.000;HaplotypeScore=3.7854;MLEAC=4;MLEAF=0.500;MQ=12.99;MQ0=346;MQRankSum=-0.595;QD=1.85;ReadPosRankSum=0.424 GT:AD:DP:GQ:PL 0/1:79,29:110:99:181,0,185 0/1:107,42:151:99:318,0,239 0/1:89,36:126:99:141,0,141 0/1:54,47:101:99:296,0,245 1 534043 . G A 829.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=5.141;DP=354;Dels=0.00;FS=0.000;HaplotypeScore=7.4218;MLEAC=4;MLEAF=0.500;MQ=15.71;MQ0=216;MQRankSum=0.505;QD=2.34;ReadPosRankSum=2.786 GT:AD:DP:GQ:PL 0/1:61,27:91:99:179,0,213 0/1:52,52:105:99:314,0,210 0/1:55,26:83:99:123,0,152 0/1:52,23:75:99:246,0,220 1 534052 . G A 46.06 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=3.685;DP=337;Dels=0.00;FS=0.000;HaplotypeScore=7.9977;MLEAC=2;MLEAF=0.250;MQ=16.07;MQ0=209;MQRankSum=-2.009;QD=0.27;ReadPosRankSum=1.235 GT:AD:DP:GQ:PL 0/0:80,10:91:30:0,30,468 0/1:71,25:97:63:63,0,442 0/0:62,14:76:30:0,30,280 0/1:61,11:73:17:17,0,476 1 534082 . A G 328.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.936;DP=267;Dels=0.00;FS=0.000;HaplotypeScore=3.0188;MLEAC=4;MLEAF=0.500;MQ=14.15;MQ0=188;MQRankSum=0.822;QD=1.23;ReadPosRankSum=1.787 GT:AD:DP:GQ:PL 0/1:63,17:80:99:121,0,181 0/1:54,13:67:97:97,0,205 0/1:56,8:64:82:82,0,114 0/1:47,9:56:61:61,0,210 1 534166 . T G 258.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-4.139;DP=288;Dels=0.00;FS=17.636;HaplotypeScore=0.6086;MLEAC=4;MLEAF=0.500;MQ=21.54;MQ0=126;MQRankSum=-0.635;QD=0.90;ReadPosRankSum=0.830 GT:AD:DP:GQ:PL 0/1:42,30:72:99:117,0,443 0/1:65,18:83:29:29,0,659 0/1:54,20:74:49:49,0,402 0/1:45,14:59:96:96,0,435 1 534192 . C T 93.38 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.471;DP=348;Dels=0.00;FS=0.623;HaplotypeScore=9.7995;MLEAC=3;MLEAF=0.375;MQ=27.61;MQ0=108;MQRankSum=-4.523;QD=0.38;ReadPosRankSum=0.940 GT:AD:DP:GQ:PL 0/1:66,13:79:25:25,0,886 0/0:81,22:103:6:0,6,1000 0/1:70,23:94:57:57,0,931 0/1:50,21:71:44:44,0,843 1 534198 . C T 98.46 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=6.327;DP=367;Dels=0.00;FS=0.947;HaplotypeScore=10.5753;MLEAC=1;MLEAF=0.125;MQ=28.30;MQ0=105;MQRankSum=-3.750;QD=1.19;ReadPosRankSum=-0.237 GT:AD:DP:GQ:PL 0/1:64,19:83:99:130,0,847 0/0:88,15:103:95:0,95,1218 0/0:88,11:99:33:0,33,1084 0/0:73,8:81:13:0,13,1032 1 534545 . G A 277.68 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=4.805;DP=190;Dels=0.00;FS=1.807;HaplotypeScore=5.8881;MLEAC=3;MLEAF=0.375;MQ=42.43;MQ0=9;MQRankSum=-4.122;QD=1.90;ReadPosRankSum=-0.479 GT:AD:DP:GQ:PL 0/1:29,9:38:89:89,0,733 0/0:37,7:44:5:0,5,870 0/1:42,13:55:99:115,0,1119 0/1:43,10:53:99:106,0,1122 1 536095 . C T 40.29 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=5.698;DP=151;Dels=0.00;FS=3.089;HaplotypeScore=1.5344;MLEAC=2;MLEAF=0.250;MQ=26.31;MQ0=21;MQRankSum=-4.633;QD=0.38;ReadPosRankSum=-1.008 GT:AD:DP:GQ:PL 0/1:29,9:39:4:4,0,632 0/1:29,7:36:1:1,0,664 0/1:23,8:31:65:65,0,289 0/0:39,6:45:84:0,84,773 1 536147 . G T 47.33 HARD_TO_VALIDATE;LowQD;LowQual AC=4;AF=0.500;AN=8;BaseQRankSum=-1.297;DP=205;Dels=0.00;FS=7.497;HaplotypeScore=2.9480;MLEAC=4;MLEAF=0.500;MQ=28.47;MQ0=30;MQRankSum=-0.537;QD=0.23;ReadPosRankSum=2.406 GT:AD:DP:GQ:PL 0/1:46,5:52:20:20,0,745 0/1:38,5:43:10:10,0,744 0/1:58,5:63:15:15,0,1084 0/1:42,4:47:34:34,0,665 1 536190 . C T 35.34 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=0.689;DP=192;Dels=0.00;FS=10.563;HaplotypeScore=2.3297;MLEAC=1;MLEAF=0.125;MQ=28.38;MQ0=29;MQRankSum=-2.342;QD=0.84;ReadPosRankSum=-0.925 GT:AD:DP:GQ:PL 0/0:39,5:44:32:0,32,822 0/1:36,6:42:67:67,0,665 0/0:67,3:70:99:0,144,1534 0/0:30,6:36:40:0,40,628 1 536208 . T A 30.39 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=0.175;DP=154;Dels=0.00;FS=1.623;HaplotypeScore=3.6779;MLEAC=1;MLEAF=0.125;MQ=28.55;MQ0=20;MQRankSum=-0.076;QD=1.09;ReadPosRankSum=-4.027 GT:AD:DP:GQ:PL 0/0:37,1:38:81:0,81,834 0/0:32,2:34:17:0,17,693 0/0:50,3:53:36:0,36,1045 0/1:25,3:28:62:62,0,367 1 536673 . G A 81.93 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.599;DP=177;Dels=0.00;FS=18.163;HaplotypeScore=0.4314;MLEAC=2;MLEAF=0.250;MQ=16.59;MQ0=86;MQRankSum=1.181;QD=0.85;ReadPosRankSum=0.065 GT:AD:DP:GQ:PL 0/0:38,5:43:27:0,27,437 0/1:41,10:51:46:46,0,558 0/0:36,2:38:24:0,24,413 0/1:39,6:45:70:70,0,365 1 536961 . T C 210.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-6.699;DP=248;Dels=0.00;FS=20.442;HaplotypeScore=1.8162;MLEAC=3;MLEAF=0.375;MQ=22.01;MQ0=46;MQRankSum=-2.724;QD=1.09;ReadPosRankSum=0.383 GT:AD:DP:GQ:PL 0/0:48,6:55:31:0,31,872 0/1:44,15:59:99:115,0,761 0/1:57,11:68:30:30,0,1069 0/1:51,15:66:99:100,0,1082 1 536986 . G T 470.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=5.954;DP=274;Dels=0.00;FS=4.761;HaplotypeScore=3.1573;MLEAC=4;MLEAF=0.500;MQ=22.46;MQ0=36;MQRankSum=-1.678;QD=1.72;ReadPosRankSum=0.014 GT:AD:DP:GQ:PL 0/1:54,12:66:44:44,0,941 0/1:48,17:65:99:214,0,875 0/1:57,12:69:87:87,0,996 0/1:57,17:74:99:158,0,1159 1 537053 . G A 175.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=5.178;DP=230;Dels=0.00;FS=5.467;HaplotypeScore=0.3281;MLEAC=4;MLEAF=0.500;MQ=12.92;MQ0=156;MQRankSum=-0.347;QD=0.76;ReadPosRankSum=-0.617 GT:AD:DP:GQ:PL 0/1:51,21:72:38:38,0,257 0/1:44,13:57:28:28,0,347 0/1:34,7:41:35:35,0,242 0/1:45,15:60:99:107,0,309 1 537191 . C G 481.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=4.101;DP=157;Dels=0.00;FS=90.477;HaplotypeScore=1.6179;MLEAC=4;MLEAF=0.500;MQ=24.79;MQ0=24;MQRankSum=-3.786;QD=3.07;ReadPosRankSum=-1.068 GT:AD:DP:GQ:PL 0/1:20,13:33:99:185,0,283 0/1:35,14:49:99:189,0,583 0/1:25,16:41:99:107,0,532 0/1:27,7:34:33:33,0,550 1 537418 . G A 105.07 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.852;DP=155;Dels=0.00;FS=15.452;HaplotypeScore=0.1446;MLEAC=2;MLEAF=0.250;MQ=16.64;MQ0=84;MQRankSum=-1.450;QD=1.46;ReadPosRankSum=-2.156 GT:AD:DP:GQ:PL 0/0:36,6:42:14:0,14,342 0/1:33,7:40:60:60,0,339 0/1:22,10:32:79:79,0,212 0/0:34,7:41:48:0,48,469 1 537468 . G T 103.03 HARD_TO_VALIDATE AC=2;AF=0.250;AN=8;BaseQRankSum=1.935;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.1972;MLEAC=2;MLEAF=0.250;MQ=15.17;MQ0=26;MQRankSum=-1.474;QD=3.68;ReadPosRankSum=1.336 GT:AD:DP:GQ:PL 0/0:13,3:16:6:0,6,53 0/1:8,4:12:51:51,0,61 0/0:8,2:10:15:0,15,143 0/1:9,7:16:59:85,0,59 1 537487 . C T 127.81 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=1.571;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=14.50;MQ0=15;MQRankSum=-0.175;QD=5.81;ReadPosRankSum=2.706 GT:AD:DP:GQ:PL 0/0:7,1:8:3:0,3,27 0/1:4,6:10:15:84,0,15 0/0:3,2:5:3:0,3,27 1/1:5,7:12:9:77,9,0 1 539738 . G C 42.80 LowQual AC=6;AF=1.00;AN=6;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=14.99;MQ0=1;QD=8.56 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:22,3,0 1/1:0,1:1:3:22,3,0 1/1:0,2:2:3:22,3,0 1 541052 . T C 149.28 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.777;DP=186;Dels=0.00;FS=57.816;HaplotypeScore=0.4138;MLEAC=3;MLEAF=0.375;MQ=26.49;MQ0=56;MQRankSum=-3.081;QD=1.05;ReadPosRankSum=0.373 GT:AD:DP:GQ:PL 0/1:33,6:40:12:12,0,594 0/1:39,7:46:45:45,0,688 0/0:38,6:44:18:0,18,680 0/1:44,12:56:99:126,0,870 1 544395 . G A 534.96 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.882;DP=186;Dels=0.00;FS=6.547;HaplotypeScore=0.7450;MLEAC=4;MLEAF=0.500;MQ=15.35;MQ0=106;MQRankSum=-0.941;QD=2.88;ReadPosRankSum=-0.160 GT:AD:DP:GQ:PL 0/1:36,7:43:24:24,0,215 0/1:36,18:54:99:291,0,233 0/1:36,8:44:64:64,0,297 0/1:32,12:44:99:188,0,356 1 544787 . G C 187.80 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.639;DP=210;Dels=0.00;FS=3.519;HaplotypeScore=1.1522;MLEAC=4;MLEAF=0.500;MQ=23.23;MQ0=74;MQRankSum=-1.598;QD=0.89;ReadPosRankSum=-0.176 GT:AD:DP:GQ:PL 0/1:45,9:54:9:9,0,618 0/1:46,11:57:67:67,0,384 0/1:35,5:40:7:7,0,189 0/1:50,9:59:99:136,0,539 1 544814 . C T 73.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=4.018;DP=201;Dels=0.00;FS=0.000;HaplotypeScore=4.3471;MLEAC=2;MLEAF=0.250;MQ=19.01;MQ0=95;MQRankSum=-1.414;QD=0.80;ReadPosRankSum=0.318 GT:AD:DP:GQ:PL 0/1:39,10:52:64:64,0,266 0/0:47,8:56:42:0,42,387 0/1:31,8:40:44:44,0,51 0/0:50,3:53:42:0,42,387 1 544815 . G A 32.44 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-1.588;DP=203;Dels=0.00;FS=0.000;HaplotypeScore=4.3471;MLEAC=2;MLEAF=0.250;MQ=18.92;MQ0=97;MQRankSum=-0.227;QD=0.29;ReadPosRankSum=-1.937 GT:AD:DP:GQ:PL 0/0:48,4:52:17:0,17,395 0/1:51,6:57:50:50,0,297 0/0:39,1:40:12:0,12,119 0/1:47,7:54:16:16,0,412 1 544940 . T A 92.02 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.350;DP=148;Dels=0.00;FS=0.000;HaplotypeScore=0.4749;MLEAC=4;MLEAF=0.500;MQ=11.36;MQ0=107;MQRankSum=1.417;QD=0.62;ReadPosRankSum=-1.350 GT:AD:DP:GQ:PL 0/1:40,4:46:23:23,0,66 0/1:33,4:39:56:56,0,79 0/1:28,5:33:28:28,0,84 0/1:26,2:29:17:17,0,50 1 545952 . T A 84.73 HARD_TO_VALIDATE AC=1;AF=0.125;AN=8;BaseQRankSum=-0.698;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=0.1663;MLEAC=1;MLEAF=0.125;MQ=14.52;MQ0=55;MQRankSum=1.193;QD=3.26;ReadPosRankSum=-2.269 GT:AD:DP:GQ:PL 0/1:19,5:26:93:116,0,93 0/0:27,5:32:12:0,12,120 0/0:23,2:25:12:0,12,129 0/0:15,2:17:15:0,15,140 1 545995 . C A 132.45 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.454;DP=187;Dels=0.00;FS=0.000;HaplotypeScore=1.7093;MLEAC=3;MLEAF=0.375;MQ=15.69;MQ0=93;MQRankSum=-0.619;QD=1.07;ReadPosRankSum=1.400 GT:AD:DP:GQ:PL 0/1:40,10:50:94:94,0,247 0/0:53,9:62:6:0,6,252 0/1:31,4:35:17:17,0,213 0/1:34,5:39:54:54,0,322 1 546004 . A G 64.94 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=0.807;DP=205;Dels=0.00;FS=19.104;HaplotypeScore=3.1930;MLEAC=2;MLEAF=0.250;MQ=16.07;MQ0=100;MQRankSum=-0.334;QD=0.60;ReadPosRankSum=-1.979 GT:AD:DP:GQ:PL 0/0:48,5:54:21:0,21,417 0/1:60,8:68:37:37,0,309 0/1:34,7:41:62:62,0,314 0/0:35,7:42:57:0,57,535 1 546197 . G A 36.03 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=0.890;DP=145;Dels=0.00;FS=0.000;HaplotypeScore=1.5915;MLEAC=2;MLEAF=0.250;MQ=17.11;MQ0=72;MQRankSum=0.084;QD=0.46;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL 0/1:39,5:44:18:18,0,301 0/1:28,7:35:52:52,0,207 0/0:24,6:30:33:0,33,314 0/0:33,3:36:45:0,45,443 1 546528 . C T 41.35 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-2.066;DP=175;Dels=0.00;FS=3.524;HaplotypeScore=1.7760;MLEAC=1;MLEAF=0.125;MQ=28.51;MQ0=59;MQRankSum=-3.117;QD=0.96;ReadPosRankSum=-1.117 GT:AD:DP:GQ:PL 0/0:39,4:43:60:0,60,623 0/1:32,11:43:73:73,0,560 0/0:32,3:35:40:0,40,672 0/0:45,8:54:23:0,23,1060 1 546697 . A G 6203.35 PASS AC=8;AF=1.00;AN=8;DP=259;Dels=0.00;FS=0.000;HaplotypeScore=2.5417;MLEAC=8;MLEAF=1.00;MQ=33.29;MQ0=8;QD=23.95 GT:AD:DP:GQ:PL 1/1:0,66:66:99:1525,150,0 1/1:0,86:86:99:1804,177,0 1/1:0,56:56:99:1466,144,0 1/1:0,51:51:99:1434,141,0 1 546732 . C T 163.33 PASS AC=1;AF=0.125;AN=8;BaseQRankSum=-1.589;DP=334;Dels=0.00;FS=76.784;HaplotypeScore=5.5379;MLEAC=1;MLEAF=0.125;MQ=32.34;MQ0=25;MQRankSum=-4.433;QD=1.97;ReadPosRankSum=-4.155 GT:AD:DP:GQ:PL 0/1:63,20:83:99:195,0,1171 0/0:83,7:90:84:0,84,1701 0/0:73,12:85:37:0,37,1773 0/0:64,12:76:44:0,44,1697 1 546802 . G C 682.03 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-5.007;DP=410;Dels=0.00;FS=137.762;HaplotypeScore=9.7613;MLEAC=4;MLEAF=0.500;MQ=26.81;MQ0=75;MQRankSum=-3.614;QD=1.66;ReadPosRankSum=1.698 GT:AD:DP:GQ:PL 0/1:67,39:106:99:412,0,874 0/1:71,33:104:79:79,0,918 0/1:65,36:102:15:15,0,915 0/1:66,32:98:99:208,0,1031 1 546805 . T C 766.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.452;DP=403;Dels=0.00;FS=151.729;HaplotypeScore=10.4984;MLEAC=4;MLEAF=0.500;MQ=26.59;MQ0=72;MQRankSum=-3.344;QD=1.90;ReadPosRankSum=2.671 GT:AD:DP:GQ:PL 0/1:61,40:105:99:379,0,845 0/1:66,32:101:56:56,0,860 0/1:58,38:98:99:107,0,769 0/1:61,36:98:99:257,0,945 1 546882 . T C 534.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.889;DP=460;Dels=0.00;FS=62.716;HaplotypeScore=7.4162;MLEAC=4;MLEAF=0.500;MQ=22.44;MQ0=146;MQRankSum=-5.555;QD=1.16;ReadPosRankSum=-3.560 GT:AD:DP:GQ:PL 0/1:65,45:115:99:125,0,1054 0/1:64,46:112:99:205,0,766 0/1:65,53:121:99:115,0,813 0/1:67,41:109:99:122,0,848 1 546925 . G A 278.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=7.901;DP=902;Dels=0.00;FS=0.878;HaplotypeScore=7.7591;MLEAC=3;MLEAF=0.375;MQ=20.75;MQ0=308;MQRankSum=-3.067;QD=0.43;ReadPosRankSum=-4.313 GT:AD:DP:GQ:PL 0/0:205,44:249:91:0,91,2198 0/1:207,33:240:26:26,0,1748 0/1:164,35:200:66:66,0,1529 0/1:170,41:213:99:221,0,1446 1 546952 . T C 2601.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-7.746;DP=939;Dels=0.00;FS=0.982;HaplotypeScore=3.9579;MLEAC=4;MLEAF=0.500;MQ=19.17;MQ0=358;MQRankSum=-2.458;QD=2.77;ReadPosRankSum=6.629 GT:AD:DP:GQ:PL 0/1:132,111:247:99:585,0,1162 0/1:129,120:250:99:728,0,1004 0/1:100,116:217:99:551,0,1063 0/1:105,119:225:99:770,0,880 1 546965 . G A 486.96 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.615;DP=937;Dels=0.00;FS=1.852;HaplotypeScore=13.1604;MLEAC=4;MLEAF=0.500;MQ=17.93;MQ0=384;MQRankSum=0.434;QD=0.52;ReadPosRankSum=0.550 GT:AD:DP:GQ:PL 0/1:214,34:250:99:227,0,1089 0/1:204,45:249:23:23,0,1376 0/1:170,34:204:99:120,0,1284 0/1:199,34:234:99:149,0,1177 1 546985 . G A 161.10 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=3.188;DP=902;Dels=0.00;FS=67.170;HaplotypeScore=10.4785;MLEAC=2;MLEAF=0.250;MQ=15.92;MQ0=421;MQRankSum=2.110;QD=0.37;ReadPosRankSum=2.434 GT:AD:DP:GQ:PL 0/1:223,25:250:99:162,0,1034 0/0:219,23:242:5:0,5,1304 0/1:171,18:189:32:32,0,1038 0/0:201,19:221:50:0,50,1141 1 547110 . C T 172.42 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.284;DP=754;Dels=0.00;FS=0.000;HaplotypeScore=14.7675;MLEAC=3;MLEAF=0.375;MQ=9.96;MQ0=526;MQRankSum=2.988;QD=0.30;ReadPosRankSum=1.498 GT:AD:DP:GQ:PL 0/1:178,14:195:9:9,0,334 0/1:176,22:200:99:139,0,113 0/0:160,11:176:30:0,30,261 0/1:166,12:180:58:58,0,128 1 547112 . G C 101.68 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-6.181;DP=742;Dels=0.01;FS=0.000;HaplotypeScore=14.4216;MLEAC=3;MLEAF=0.375;MQ=10.08;MQ0=511;MQRankSum=2.432;QD=0.18;ReadPosRankSum=1.373 GT:AD:DP:GQ:PL 0/1:179,17:196:4:4,0,366 0/1:171,22:195:99:118,0,154 0/0:150,14:165:30:0,30,279 0/1:167,13:180:12:12,0,300 1 547133 . G A 36.14 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=1.816;DP=858;Dels=0.00;FS=0.000;HaplotypeScore=4.5250;MLEAC=2;MLEAF=0.250;MQ=12.42;MQ0=516;MQRankSum=-0.673;QD=0.09;ReadPosRankSum=3.848 GT:AD:DP:GQ:PL 0/0:224,19:246:74:0,74,996 0/0:207,10:218:93:0,93,916 0/1:165,23:188:55:55,0,484 0/1:181,25:206:15:15,0,632 1 547146 . C T 149.14 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=3.536;DP=889;Dels=0.00;FS=3.731;HaplotypeScore=7.5274;MLEAC=3;MLEAF=0.375;MQ=13.80;MQ0=491;MQRankSum=-0.557;QD=0.23;ReadPosRankSum=-1.879 GT:AD:DP:GQ:PL 0/0:204,43:248:22:0,22,691 0/1:195,28:224:5:5,0,781 0/1:161,44:208:31:31,0,570 0/1:151,56:207:99:146,0,598 1 547160 . T C 67.21 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-9.876;DP=907;Dels=0.00;FS=6.374;HaplotypeScore=8.3699;MLEAC=3;MLEAF=0.375;MQ=14.87;MQ0=452;MQRankSum=1.846;QD=0.10;ReadPosRankSum=1.080 GT:AD:DP:GQ:PL 0/1:214,35:249:78:78,0,1059 0/1:219,19:240:5:5,0,1015 0/0:187,24:212:26:0,26,1014 0/1:172,32:205:17:17,0,968 1 547185 . G T 314.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-2.557;DP=908;Dels=0.00;FS=11.036;HaplotypeScore=3.3190;MLEAC=4;MLEAF=0.500;MQ=14.34;MQ0=472;MQRankSum=-0.287;QD=0.35;ReadPosRankSum=-1.141 GT:AD:DP:GQ:PL 0/1:214,35:249:99:99,0,843 0/1:195,40:238:77:77,0,1023 0/1:169,30:199:53:53,0,1072 0/1:184,37:221:99:118,0,895 1 547214 . C T 135.42 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=5.777;DP=844;Dels=0.00;FS=8.982;HaplotypeScore=9.7856;MLEAC=3;MLEAF=0.375;MQ=12.42;MQ0=523;MQRankSum=2.303;QD=0.22;ReadPosRankSum=1.331 GT:AD:DP:GQ:PL 0/1:225,18:244:42:42,0,555 0/0:206,11:219:11:0,11,689 0/1:163,15:178:83:83,0,601 0/1:188,13:202:44:44,0,472 1 547237 . G A 446.96 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.491;DP=781;Dels=0.00;FS=25.348;HaplotypeScore=1.9678;MLEAC=4;MLEAF=0.500;MQ=9.65;MQ0=581;MQRankSum=-0.424;QD=0.57;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL 0/1:203,44:247:99:148,0,344 0/1:159,34:193:24:24,0,332 0/1:120,41:161:99:213,0,299 0/1:133,47:180:94:94,0,337 1 547250 . C T 223.36 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.142;DP=723;Dels=0.00;FS=10.636;HaplotypeScore=0.1663;MLEAC=3;MLEAF=0.375;MQ=6.53;MQ0=590;MQRankSum=-0.896;QD=0.41;ReadPosRankSum=1.459 GT:AD:DP:GQ:PL 0/1:187,36:226:99:108,0,153 0/1:153,30:184:4:4,0,149 0/1:109,29:140:99:144,0,137 0/0:140,32:173:33:0,33,303 1 547484 . C T 34.24 HARD_TO_VALIDATE;LowQD;LowQual AC=5;AF=0.625;AN=8;BaseQRankSum=5.111;DP=808;Dels=0.00;FS=0.000;HaplotypeScore=2.3192;MLEAC=5;MLEAF=0.625;MQ=4.13;MQ0=613;MQRankSum=2.773;QD=0.06;ReadPosRankSum=-4.773 GT:AD:DP:GQ:PL 1/1:205,34:241:3:25,3,0 0/1:184,22:209:17:17,0,27 1/1:131,23:154:3:23,3,0 0/0:178,23:203:3:0,3,24 1 547562 . C T 46.66 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.750;AN=4;BaseQRankSum=0.733;DP=161;Dels=0.00;FS=0.000;HaplotypeScore=8.1579;MLEAC=3;MLEAF=0.750;MQ=7.01;MQ0=123;MQRankSum=1.890;QD=0.45;ReadPosRankSum=1.273 GT:AD:DP:GQ:PL 1/1:32,17:51:6:59,6,0 ./. ./. 0/1:48,4:52:15:15,0,58 1 547564 . A C 46.66 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.750;AN=4;BaseQRankSum=0.634;DP=150;Dels=0.00;FS=0.000;HaplotypeScore=8.6050;MLEAC=3;MLEAF=0.750;MQ=7.26;MQ0=114;MQRankSum=2.124;QD=0.49;ReadPosRankSum=0.783 GT:AD:DP:GQ:PL 1/1:37,7:45:6:59,6,0 ./. ./. 0/1:49,2:51:15:15,0,58 1 547601 . G T 36.89 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=-0.975;DP=382;Dels=0.00;FS=9.457;HaplotypeScore=2.8949;MLEAC=3;MLEAF=0.375;MQ=9.82;MQ0=269;MQRankSum=0.598;QD=0.12;ReadPosRankSum=0.526 GT:AD:DP:GQ:PL 0/1:82,18:100:12:12,0,255 0/1:70,28:98:13:13,0,269 0/0:64,14:78:11:0,11,261 0/1:86,19:105:45:45,0,326 1 547782 . C T 98.95 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=4.701;DP=629;Dels=0.00;FS=20.213;HaplotypeScore=12.7331;MLEAC=3;MLEAF=0.375;MQ=8.87;MQ0=331;MQRankSum=3.986;QD=0.23;ReadPosRankSum=-2.929 GT:AD:DP:GQ:PL 0/0:187,4:192:14:0,14,322 0/1:162,11:174:92:92,0,272 0/1:111,6:119:33:33,0,108 0/1:138,6:144:7:7,0,320 1 554354 . G A 32.71 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=3.014;DP=174;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=6.98;MQ0=153;MQRankSum=0.289;QD=0.25;ReadPosRankSum=0.950 GT:AD:DP:GQ:PL 0/0:43,2:45:3:0,3,25 0/1:45,7:52:18:18,0,44 0/1:35,3:38:13:13,0,97 0/1:36,3:39:33:33,0,106 1 554662 . A C 98.91 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.905;DP=198;Dels=0.00;FS=24.626;HaplotypeScore=1.1957;MLEAC=2;MLEAF=0.250;MQ=15.71;MQ0=121;MQRankSum=-3.307;QD=1.05;ReadPosRankSum=-0.103 GT:AD:DP:GQ:PL 0/0:41,7:48:27:0,27,470 0/1:41,11:52:65:65,0,214 0/1:30,12:42:68:68,0,234 0/0:46,8:54:36:0,36,524 1 554735 . G A 176.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=4.404;DP=167;Dels=0.00;FS=32.803;HaplotypeScore=1.4230;MLEAC=3;MLEAF=0.375;MQ=18.39;MQ0=74;MQRankSum=-2.121;QD=1.40;ReadPosRankSum=-0.507 GT:AD:DP:GQ:PL 0/0:35,6:41:39:0,39,534 0/1:34,11:45:38:38,0,265 0/1:28,13:41:97:97,0,353 0/1:30,10:40:76:76,0,509 1 554797 . C T 192.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.519;DP=222;Dels=0.00;FS=0.000;HaplotypeScore=1.9418;MLEAC=3;MLEAF=0.375;MQ=31.24;MQ0=47;MQRankSum=-7.742;QD=1.16;ReadPosRankSum=0.393 GT:AD:DP:GQ:PL 0/1:34,16:50:30:30,0,743 0/0:40,15:55:48:0,48,1149 0/1:34,19:53:50:50,0,832 0/1:37,26:63:99:147,0,1007 1 555165 . T G 557.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.047;DP=239;Dels=0.00;FS=0.000;HaplotypeScore=0.4811;MLEAC=4;MLEAF=0.500;MQ=18.07;MQ0=105;MQRankSum=-1.531;QD=2.33;ReadPosRankSum=-1.851 GT:AD:DP:GQ:PL 0/1:29,15:44:89:89,0,279 0/1:46,25:71:99:280,0,554 0/1:43,17:60:46:46,0,398 0/1:47,17:64:99:175,0,527 1 555561 . C T 73.97 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=3.388;DP=279;Dels=0.00;FS=0.000;HaplotypeScore=0.2479;MLEAC=3;MLEAF=0.375;MQ=12.45;MQ0=179;MQRankSum=0.444;QD=0.35;ReadPosRankSum=0.097 GT:AD:DP:GQ:PL 0/0:63,6:69:22:0,22,368 0/1:64,10:74:52:52,0,468 0/1:51,6:57:24:24,0,525 0/1:68,11:79:32:32,0,439 1 557155 . C T 283.98 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-2.530;DP=233;Dels=0.00;FS=14.674;HaplotypeScore=1.3223;MLEAC=4;MLEAF=0.500;MQ=14.81;MQ0=126;MQRankSum=1.637;QD=1.22;ReadPosRankSum=1.392 GT:AD:DP:GQ:PL 0/1:55,9:64:61:61,0,508 0/1:52,10:62:20:20,0,427 0/1:35,15:50:99:210,0,292 0/1:47,10:57:25:25,0,409 1 559135 . T G 211.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-6.557;DP=160;Dels=0.00;FS=7.335;HaplotypeScore=1.2295;MLEAC=4;MLEAF=0.500;MQ=18.28;MQ0=79;MQRankSum=0.124;QD=1.32;ReadPosRankSum=1.798 GT:AD:DP:GQ:PL 0/1:40,5:46:28:28,0,389 0/1:34,7:41:45:45,0,376 0/1:20,7:27:99:117,0,232 0/1:39,7:46:54:54,0,362 1 559368 . A G 723.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.547;DP=218;Dels=0.00;FS=4.073;HaplotypeScore=3.0723;MLEAC=4;MLEAF=0.500;MQ=23.27;MQ0=40;MQRankSum=-3.604;QD=3.32;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL 0/1:36,17:53:99:276,0,569 0/1:44,9:53:94:94,0,993 0/1:42,13:55:99:216,0,690 0/1:44,12:56:99:170,0,720 1 559631 . A G 126.92 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.003;DP=169;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=16.76;MQ0=84;MQRankSum=-2.399;QD=1.09;ReadPosRankSum=0.693 GT:AD:DP:GQ:PL 0/1:33,7:40:99:100,0,329 0/1:32,6:38:30:30,0,346 0/1:35,3:38:31:31,0,359 0/0:49,4:53:28:0,28,680 1 559889 . A G 57.06 HARD_TO_VALIDATE AC=2;AF=0.250;AN=8;BaseQRankSum=-0.384;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=2.5685;MLEAC=2;MLEAF=0.250;MQ=33.52;MQ0=17;MQRankSum=-2.177;QD=1.63;ReadPosRankSum=2.214 GT:AD:DP:GQ:PL 0/1:14,5:19:26:26,0,299 0/1:11,5:16:65:65,0,144 0/0:9,0:9:18:0,18,195 0/0:10,3:13:18:0,18,173 1 562020 . T C 473.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.620;DP=94;Dels=0.00;FS=17.996;HaplotypeScore=6.3382;MLEAC=4;MLEAF=0.500;MQ=31.46;MQ0=29;MQRankSum=1.532;QD=5.04;ReadPosRankSum=0.667 GT:AD:DP:GQ:PL 0/1:10,5:15:74:74,0,168 0/1:22,9:32:99:216,0,168 0/1:13,5:18:73:73,0,114 0/1:18,10:28:99:143,0,214 1 562908 . A G 54.80 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=9.98;MQ0=10;QD=4.98 GT:AD:DP:GQ:PL ./. 1/1:0,4:4:3:22,3,0 1/1:1,2:3:3:28,3,0 1/1:0,4:4:3:28,3,0 1 563599 . C T 123.80 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=3.016;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=11.93;MQ0=44;MQRankSum=1.493;QD=3.26;ReadPosRankSum=-0.935 GT:AD:DP:GQ:PL 0/1:11,5:16:16:81,0,16 0/0:17,2:19:15:0,15,130 0/1:8,5:13:20:48,0,20 1/1:8,1:9:3:29,3,0 1 563625 . T C 502.53 PASS AC=8;AF=1.00;AN=8;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=22.12;MQ0=1;QD=22.84 GT:AD:DP:GQ:PL 1/1:0,7:7:15:141,15,0 1/1:0,5:5:15:134,15,0 1/1:0,4:4:12:114,12,0 1/1:0,6:6:15:139,15,0 1 567242 . G A 123.34 HARD_TO_VALIDATE AC=1;AF=0.125;AN=8;BaseQRankSum=-0.458;DP=396;Dels=0.00;FS=4.405;HaplotypeScore=28.8368;MLEAC=1;MLEAF=0.125;MQ=20.28;MQ0=265;MQRankSum=-1.212;QD=3.25;ReadPosRankSum=-3.853 GT:AD:DP:GQ:PL 0/1:31,7:38:99:155,0,254 0/0:128,1:129:60:0,60,671 0/0:96,1:97:90:0,90,1019 0/0:126,6:132:27:0,27,978 1 571623 . T G 1194.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.563;DP=200;Dels=0.00;FS=0.000;HaplotypeScore=2.3366;MLEAC=4;MLEAF=0.500;MQ=26.44;MQ0=105;MQRankSum=-0.168;QD=5.97;ReadPosRankSum=0.332 GT:AD:DP:GQ:PL 0/1:20,29:49:99:385,0,207 0/1:30,29:59:99:189,0,459 0/1:21,22:43:99:217,0,291 0/1:21,28:49:99:436,0,227 1 571629 . T C 1474.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.405;DP=190;Dels=0.00;FS=0.000;HaplotypeScore=2.3788;MLEAC=4;MLEAF=0.500;MQ=25.58;MQ0=105;MQRankSum=1.089;QD=7.76;ReadPosRankSum=0.496 GT:AD:DP:GQ:PL 0/1:13,32:45:86:441,0,86 0/1:23,33:56:99:310,0,293 0/1:13,26:39:99:269,0,207 0/1:15,35:50:99:487,0,180 1 571646 . G A 321.93 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-3.645;DP=187;Dels=0.00;FS=0.000;HaplotypeScore=1.2309;MLEAC=4;MLEAF=0.500;MQ=24.54;MQ0=109;MQRankSum=-0.074;QD=2.21;ReadPosRankSum=1.264 GT:AD:DP:GQ:PL 0/1:35,11:46:99:116,0,433 0/1:38,13:51:72:72,0,466 0/0:34,7:41:2:0,2,397 0/1:33,16:49:99:165,0,452 1 571672 . T C 100.27 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.663;DP=180;Dels=0.00;FS=0.000;HaplotypeScore=0.2497;MLEAC=4;MLEAF=0.500;MQ=18.85;MQ0=131;MQRankSum=0.825;QD=0.56;ReadPosRankSum=1.068 GT:AD:DP:GQ:PL 0/1:36,5:41:35:35,0,275 0/1:41,4:46:9:9,0,202 0/1:36,9:45:44:44,0,219 0/1:38,10:48:44:44,0,377 1 577193 . G A 37.19 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=3.062;DP=149;Dels=0.00;FS=2.448;HaplotypeScore=0.9072;MLEAC=1;MLEAF=0.125;MQ=9.83;MQ0=111;MQRankSum=-1.902;QD=0.85;ReadPosRankSum=-2.222 GT:AD:DP:GQ:PL 0/0:33,3:36:5:0,5,203 0/0:31,2:33:15:0,15,126 0/0:35,1:36:18:0,18,152 0/1:39,5:44:68:68,0,123 1 588788 . C T 366.04 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-1.189;DP=170;Dels=0.00;FS=0.000;HaplotypeScore=1.3744;MLEAC=3;MLEAF=0.375;MQ=21.65;MQ0=49;MQRankSum=-3.022;QD=2.69;ReadPosRankSum=0.190 GT:AD:DP:GQ:PL 0/0:29,5:34:4:0,4,463 0/1:32,9:41:99:122,0,607 0/1:34,8:42:76:76,0,484 0/1:40,12:52:99:200,0,537 1 591818 . G A 187.47 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=4.866;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=0.2487;MLEAC=4;MLEAF=0.500;MQ=20.43;MQ0=61;MQRankSum=-0.013;QD=2.31;ReadPosRankSum=-0.213 GT:AD:DP:GQ:PL 0/1:18,8:26:68:68,0,106 0/0:20,6:26:1:0,1,210 0/1:22,7:29:99:111,0,230 0/1:22,4:26:39:39,0,131 1 594361 . A C 143.91 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.988;DP=158;Dels=0.00;FS=0.000;HaplotypeScore=0.7444;MLEAC=4;MLEAF=0.500;MQ=11.89;MQ0=110;MQRankSum=1.107;QD=0.91;ReadPosRankSum=-0.679 GT:AD:DP:GQ:PL 0/1:32,6:38:32:32,0,288 0/1:43,4:47:4:4,0,129 0/1:26,7:33:30:30,0,120 0/1:32,8:40:96:109,0,96 1 598588 . T C 212.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.549;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=1.0548;MLEAC=4;MLEAF=0.500;MQ=12.84;MQ0=71;MQRankSum=-1.925;QD=1.72;ReadPosRankSum=-0.272 GT:AD:DP:GQ:PL 0/1:23,5:28:63:63,0,162 0/1:25,8:33:84:84,0,159 0/1:25,5:30:66:66,0,140 0/1:27,6:33:32:32,0,230 1 598770 . T C 273.96 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-3.943;DP=127;Dels=0.00;FS=0.000;HaplotypeScore=0.2467;MLEAC=4;MLEAF=0.500;MQ=13.24;MQ0=71;MQRankSum=-0.592;QD=2.16;ReadPosRankSum=0.288 GT:AD:DP:GQ:PL 0/1:21,7:28:99:121,0,112 0/1:26,4:30:32:32,0,238 0/1:20,10:30:99:131,0,131 0/1:30,9:39:22:22,0,146 1 601841 . G C 190.94 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=3.213;DP=183;Dels=0.00;FS=72.478;HaplotypeScore=0.9450;MLEAC=3;MLEAF=0.375;MQ=24.65;MQ0=89;MQRankSum=-0.770;QD=1.27;ReadPosRankSum=-1.492 GT:AD:DP:GQ:PL 0/1:45,8:53:99:112,0,506 0/0:31,2:33:24:0,24,530 0/1:43,8:51:83:83,0,459 0/1:41,5:46:30:30,0,597 1 603023 . C A 91.91 HARD_TO_VALIDATE AC=1;AF=0.125;AN=8;BaseQRankSum=1.216;DP=110;Dels=0.00;FS=10.183;HaplotypeScore=1.5623;MLEAC=1;MLEAF=0.125;MQ=18.69;MQ0=47;MQRankSum=-0.037;QD=2.63;ReadPosRankSum=-0.755 GT:AD:DP:GQ:PL 0/0:21,1:22:1:0,1,198 0/0:27,2:30:1:0,1,371 0/0:21,2:23:24:0,24,221 0/1:28,7:35:99:120,0,324 1 622162 . A G 45.54 HARD_TO_VALIDATE;LowQD;LowQual AC=4;AF=0.500;AN=8;BaseQRankSum=-2.938;DP=112;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=8.05;MQ0=97;MQRankSum=1.501;QD=0.51;ReadPosRankSum=-0.588 GT:AD:DP:GQ:PL 1/1:21,1:22:3:28,3,0 0/1:28,3:31:36:36,0,93 0/0:22,1:23:9:0,9,77 0/1:34,2:36:15:15,0,72 1 622348 . T C 72.52 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.405;DP=109;Dels=0.00;FS=0.000;HaplotypeScore=0.2080;MLEAC=4;MLEAF=0.500;MQ=10.29;MQ0=87;MQRankSum=0.037;QD=0.67;ReadPosRankSum=0.479 GT:AD:DP:GQ:PL 0/1:25,4:29:14:14,0,97 0/1:26,3:29:64:65,0,64 0/1:23,2:25:8:8,0,117 0/1:22,3:26:17:17,0,71 1 622663 . T C 41.94 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=1.691;DP=219;Dels=0.00;FS=82.572;HaplotypeScore=1.2356;MLEAC=2;MLEAF=0.250;MQ=17.07;MQ0=90;MQRankSum=2.720;QD=0.41;ReadPosRankSum=-0.847 GT:AD:DP:GQ:PL 0/1:42,9:51:23:23,0,578 0/1:44,7:51:53:53,0,592 0/0:55,5:60:49:0,49,827 0/0:54,3:57:61:0,61,759 1 626579 . G A 52.33 HARD_TO_VALIDATE AC=1;AF=0.125;AN=8;BaseQRankSum=-3.665;DP=160;Dels=0.00;FS=28.682;HaplotypeScore=1.6665;MLEAC=1;MLEAF=0.125;MQ=40.42;MQ0=22;MQRankSum=-6.318;QD=1.80;ReadPosRankSum=-1.521 GT:AD:DP:GQ:PL 0/1:20,9:29:84:84,0,551 0/0:46,11:57:99:0,106,1419 0/0:23,10:33:42:0,42,686 0/0:29,11:40:37:0,37,828 1 628140 . T C 138.03 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-6.061;DP=184;Dels=0.00;FS=0.000;HaplotypeScore=0.9930;MLEAC=4;MLEAF=0.500;MQ=15.87;MQ0=84;MQRankSum=0.247;QD=0.75;ReadPosRankSum=-0.812 GT:AD:DP:GQ:PL 0/1:36,6:42:40:40,0,412 0/1:40,8:48:87:87,0,358 0/1:42,6:48:15:15,0,440 0/1:38,8:46:28:28,0,507 1 632630 . A G 102.49 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.395;DP=145;Dels=0.00;FS=40.584;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=8.62;MQ0=128;MQRankSum=-3.512;QD=1.09;ReadPosRankSum=-0.818 GT:AD:DP:GQ:PL 0/0:49,2:51:3:0,3,27 0/1:31,4:35:48:48,0,160 1/1:17,2:19:3:25,3,0 0/1:36,4:40:39:61,0,39 1 632709 . C T 512.41 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=2.069;DP=109;Dels=0.00;FS=11.139;HaplotypeScore=0.7400;MLEAC=7;MLEAF=0.875;MQ=9.68;MQ0=83;MQRankSum=-0.241;QD=4.70;ReadPosRankSum=0.914 GT:AD:DP:GQ:PL 1/1:19,5:24:12:102,12,0 0/1:19,5:24:13:86,0,13 1/1:23,6:29:12:102,12,0 1/1:22,10:32:30:253,30,0 1 633277 . C T 220.06 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=1.423;DP=89;Dels=0.00;FS=10.414;HaplotypeScore=0.2467;MLEAC=7;MLEAF=0.875;MQ=7.93;MQ0=78;MQRankSum=1.107;QD=2.47;ReadPosRankSum=-1.107 GT:AD:DP:GQ:PL 1/1:23,4:27:3:25,3,0 0/1:14,2:16:19:19,0,19 1/1:14,3:17:9:83,9,0 1/1:18,11:29:15:123,15,0 1 636318 . G A 36.33 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.28;MQ0=0;QD=18.16 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:61,6,0 ./. 1 645780 . A G 63.34 HARD_TO_VALIDATE;LowQD AC=3;AF=0.500;AN=6;BaseQRankSum=0.890;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.3245;MLEAC=3;MLEAF=0.500;MQ=8.91;MQ0=54;MQRankSum=0.421;QD=1.09;ReadPosRankSum=1.171 GT:AD:DP:GQ:PL 0/1:11,4:15:49:73,0,49 0/1:21,2:23:5:5,0,99 ./. 0/1:19,1:20:14:14,0,36 1 650097 . A G 196.42 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=131;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=4.81;MQ0=121;QD=1.50 GT:AD:DP:GQ:PL 1/1:26,4:30:3:22,3,0 1/1:27,11:38:12:89,12,0 1/1:16,8:24:9:65,9,0 1/1:28,11:39:6:45,6,0 1 650823 . A G 77.06 HARD_TO_VALIDATE;LowQD AC=4;AF=0.667;AN=6;BaseQRankSum=0.358;DP=159;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=6.35;MQ0=154;MQRankSum=1.231;QD=0.93;ReadPosRankSum=-0.358 GT:AD:DP:GQ:PL ./. 1/1:38,4:42:6:70,6,0 1/1:36,5:41:3:36,3,0 0/0:33,5:38:3:0,3,35 1 651054 . A G 192.12 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=1.291;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=0.2487;MLEAC=3;MLEAF=0.375;MQ=16.31;MQ0=99;MQRankSum=-0.787;QD=2.11;ReadPosRankSum=0.409 GT:AD:DP:GQ:PL 0/1:25,4:29:51:51,0,120 0/1:28,9:37:43:117,0,43 0/1:20,5:25:58:58,0,91 0/0:30,1:31:15:0,15,159 1 651077 . T C 210.77 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=1.109;DP=113;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.625;MQ=12.64;MQ0=99;MQRankSum=0.965;QD=1.87;ReadPosRankSum=0.471 GT:AD:DP:GQ:PL 0/1:20,6:27:23:93,0,23 0/1:33,2:35:19:19,0,89 0/1:24,3:27:23:28,0,23 1/1:21,3:24:9:104,9,0 1 651149 . C T 448.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.924;DP=144;Dels=0.00;FS=0.000;HaplotypeScore=0.5834;MLEAC=4;MLEAF=0.500;MQ=23.80;MQ0=97;MQRankSum=-2.562;QD=3.12;ReadPosRankSum=1.045 GT:AD:DP:GQ:PL 0/1:23,5:29:99:115,0,118 0/1:38,6:44:99:126,0,137 0/1:30,7:37:99:140,0,138 0/1:27,7:34:99:100,0,176 1 657788 . G C 1329.64 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.842;DP=117;Dels=0.00;FS=9.226;HaplotypeScore=0.9385;MLEAC=8;MLEAF=1.00;MQ=16.48;MQ0=53;MQRankSum=2.128;QD=11.36;ReadPosRankSum=-1.969 GT:AD:DP:GQ:PL 1/1:14,25:39:60:536,60,0 1/1:9,12:21:6:219,6,0 1/1:9,18:27:18:338,18,0 1/1:13,17:30:30:262,30,0 1 660078 . G A 146.77 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=183;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=4.07;MQ0=173;QD=1.65 GT:AD:DP:GQ:PL 1/1:27,10:37:9:74,9,0 ./. ./. 1/1:40,12:52:12:98,12,0 1 662029 . G A 141.07 HARD_TO_VALIDATE;LowQD AC=5;AF=0.833;AN=6;BaseQRankSum=0.747;DP=151;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.833;MQ=4.83;MQ0=143;MQRankSum=0.747;QD=1.23;ReadPosRankSum=-0.747 GT:AD:DP:GQ:PL 1/1:24,6:30:9:77,9,0 0/1:38,3:41:17:42,0,17 ./. 1/1:32,12:44:6:51,6,0 1 662201 . G A 744.51 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.628;DP=137;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=10.30;MQ0=104;MQRankSum=1.418;QD=5.43;ReadPosRankSum=-0.473 GT:AD:DP:GQ:PL 1/1:15,12:28:9:79,9,0 1/1:26,16:43:36:315,36,0 1/1:21,11:32:24:218,24,0 1/1:19,14:33:18:158,18,0 1 662857 . G A 1573.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.777;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=0.7446;MLEAC=8;MLEAF=1.00;MQ=24.47;MQ0=34;MQRankSum=1.291;QD=15.58;ReadPosRankSum=-0.094 GT:AD:DP:GQ:PL 1/1:9,18:27:42:426,42,0 1/1:8,16:24:30:335,30,0 1/1:10,14:24:27:282,27,0 1/1:7,19:26:51:556,51,0 1 663097 . G C 1959.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=108;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=19.44;MQ0=29;QD=18.14 GT:AD:DP:GQ:PL 1/1:8,17:25:42:375,42,0 1/1:0,18:18:51:473,51,0 1/1:12,19:31:45:404,45,0 1/1:3,31:34:81:733,81,0 1 663150 . C T 551.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.050;DP=89;Dels=0.00;FS=4.876;HaplotypeScore=2.3304;MLEAC=4;MLEAF=0.500;MQ=19.92;MQ0=19;MQRankSum=-0.715;QD=6.20;ReadPosRankSum=1.629 GT:AD:DP:GQ:PL 0/1:15,9:24:99:142,0,191 0/1:7,11:18:99:101,0,108 0/1:14,10:24:96:180,0,96 0/1:12,11:23:99:161,0,126 1 663412 . G A 395.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.356;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=14.48;MQ0=56;MQRankSum=-0.894;QD=4.08;ReadPosRankSum=-0.785 GT:AD:DP:GQ:PL 0/1:9,5:15:38:67,0,38 0/1:17,10:27:78:150,0,78 0/1:22,6:28:79:111,0,79 0/1:20,6:27:99:100,0,179 1 664271 . C A 332.30 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=0.971;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=0.1446;MLEAC=7;MLEAF=0.875;MQ=8.76;MQ0=83;MQRankSum=-1.656;QD=3.16;ReadPosRankSum=1.656 GT:AD:DP:GQ:PL 0/1:18,10:28:35:83,0,35 1/1:16,16:32:18:153,18,0 1/1:12,11:23:6:51,6,0 1/1:6,14:20:9:76,9,0 1 664834 . T G 64.47 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=10.62;MQ0=12;QD=4.61 GT:AD:DP:GQ:PL 1/1:0,9:9:6:43,6,0 1/1:0,5:5:6:46,6,0 ./. ./. 1 667666 . T A 700.66 PASS AC=8;AF=1.00;AN=8;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.3281;MLEAC=8;MLEAF=1.00;MQ=33.49;MQ0=2;QD=25.95 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1/1:0,7:7:18:199,18,0 1/1:0,8:8:18:208,18,0 1/1:0,10:10:24:270,24,0 1 669028 . A T 55.33 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.149;DP=173;Dels=0.00;FS=22.271;HaplotypeScore=1.1637;MLEAC=2;MLEAF=0.250;MQ=18.34;MQ0=90;MQRankSum=-3.995;QD=0.62;ReadPosRankSum=-1.052 GT:AD:DP:GQ:PL 0/0:38,1:39:27:0,27,439 0/0:42,3:45:10:0,10,398 0/1:34,6:40:57:57,0,361 0/1:40,8:48:32:32,0,422 1 669590 . G T 138.56 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=-5.020;DP=152;Dels=0.00;FS=45.619;HaplotypeScore=1.4448;MLEAC=2;MLEAF=0.250;MQ=34.68;MQ0=3;MQRankSum=-1.356;QD=1.75;ReadPosRankSum=-0.966 GT:AD:DP:GQ:PL 0/0:33,3:36:4:0,4,743 0/0:34,3:37:14:0,14,927 0/1:36,6:42:59:59,0,984 0/1:29,8:37:99:112,0,710 1 672209 . G A 495.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=4.650;DP=297;Dels=0.00;FS=0.000;HaplotypeScore=0.7118;MLEAC=4;MLEAF=0.500;MQ=26.81;MQ0=41;MQRankSum=-4.356;QD=1.67;ReadPosRankSum=0.803 GT:AD:DP:GQ:PL 0/1:50,17:67:99:254,0,866 0/1:66,13:79:60:60,0,1262 0/1:61,11:72:42:42,0,1333 0/1:60,19:79:99:172,0,1058 1 672330 . G C 83.52 HARD_TO_VALIDATE AC=1;AF=0.125;AN=8;BaseQRankSum=2.786;DP=205;Dels=0.00;FS=3.847;HaplotypeScore=0.2892;MLEAC=1;MLEAF=0.125;MQ=12.56;MQ0=129;MQRankSum=-1.462;QD=1.90;ReadPosRankSum=1.517 GT:AD:DP:GQ:PL 0/1:34,10:44:99:115,0,212 0/0:53,2:55:12:0,12,426 0/0:41,4:45:19:0,19,338 0/0:54,7:61:29:0,29,412 1 672663 . T G 736.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-8.605;DP=260;Dels=0.00;FS=0.000;HaplotypeScore=1.7242;MLEAC=4;MLEAF=0.500;MQ=18.92;MQ0=145;MQRankSum=-3.308;QD=2.83;ReadPosRankSum=-0.253 GT:AD:DP:GQ:PL 0/1:41,20:61:99:131,0,250 0/1:51,26:77:99:246,0,535 0/1:49,19:68:99:172,0,389 0/1:39,15:54:99:220,0,437 1 672823 . C G 280.93 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=5.049;DP=249;Dels=0.00;FS=35.168;HaplotypeScore=1.6091;MLEAC=3;MLEAF=0.375;MQ=35.87;MQ0=59;MQRankSum=-8.119;QD=1.61;ReadPosRankSum=-4.355 GT:AD:DP:GQ:PL 0/1:35,26:61:24:24,0,829 0/0:52,23:75:27:0,27,1321 0/1:34,17:51:80:80,0,936 0/1:36,25:62:99:211,0,999 1 672854 . G C 81.36 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.067;DP=261;Dels=0.00;FS=65.513;HaplotypeScore=2.4125;MLEAC=4;MLEAF=0.500;MQ=34.91;MQ0=46;MQRankSum=-5.321;QD=0.31;ReadPosRankSum=1.623 GT:AD:DP:GQ:PL 0/1:37,13:51:30:30,0,652 0/1:56,15:71:33:33,0,1272 0/1:56,13:69:8:8,0,1443 0/1:56,14:70:42:42,0,1315 1 673117 . T C 756.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.227;DP=210;Dels=0.00;FS=20.317;HaplotypeScore=2.0838;MLEAC=4;MLEAF=0.500;MQ=33.36;MQ0=10;MQRankSum=-10.124;QD=3.60;ReadPosRankSum=0.595 GT:AD:DP:GQ:PL 0/1:26,16:42:99:202,0,645 0/1:40,15:55:99:162,0,1131 0/1:44,19:63:99:164,0,1247 0/1:32,17:49:99:261,0,892 1 673223 . T G 307.32 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-2.115;DP=171;Dels=0.00;FS=16.992;HaplotypeScore=0.7368;MLEAC=3;MLEAF=0.375;MQ=22.97;MQ0=60;MQRankSum=0.255;QD=2.46;ReadPosRankSum=-1.042 GT:AD:DP:GQ:PL 0/1:26,5:31:39:39,0,291 0/0:36,10:46:12:0,12,647 0/1:26,12:38:64:64,0,386 0/1:41,15:56:99:238,0,655 1 673236 . G T 90.42 HARD_TO_VALIDATE AC=1;AF=0.125;AN=8;BaseQRankSum=-0.540;DP=148;Dels=0.00;FS=28.220;HaplotypeScore=0.7051;MLEAC=1;MLEAF=0.125;MQ=22.78;MQ0=47;MQRankSum=0.033;QD=1.85;ReadPosRankSum=0.692 GT:AD:DP:GQ:PL 0/0:26,1:27:15:0,15,331 0/0:35,5:40:42:0,42,642 0/0:27,5:32:23:0,23,500 0/1:39,10:49:99:122,0,613 1 673327 . G A 907.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=3.178;DP=273;Dels=0.00;FS=135.332;HaplotypeScore=1.3901;MLEAC=4;MLEAF=0.500;MQ=24.88;MQ0=96;MQRankSum=-7.473;QD=3.33;ReadPosRankSum=0.508 GT:AD:DP:GQ:PL 0/1:28,18:46:99:99,0,713 0/1:42,36:78:99:332,0,900 0/1:30,44:74:99:275,0,476 0/1:43,32:75:99:234,0,748 1 673712 . C T 247.32 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.268;DP=345;Dels=0.00;FS=1.273;HaplotypeScore=1.5077;MLEAC=3;MLEAF=0.375;MQ=19.21;MQ0=152;MQRankSum=2.786;QD=0.99;ReadPosRankSum=1.470 GT:AD:DP:GQ:PL 0/1:71,7:78:10:10,0,671 0/0:88,8:96:77:0,77,1547 0/1:57,15:72:99:221,0,748 0/1:84,15:99:50:50,0,1285 1 674421 . A T 1179.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.485;DP=214;Dels=0.00;FS=43.175;HaplotypeScore=5.5839;MLEAC=4;MLEAF=0.500;MQ=41.93;MQ0=28;MQRankSum=-9.195;QD=5.51;ReadPosRankSum=-0.587 GT:AD:DP:GQ:PL 0/1:23,19:42:99:355,0,609 0/1:27,32:59:99:416,0,732 0/1:36,15:51:99:124,0,991 0/1:36,26:62:99:317,0,1047 1 674434 . A T 705.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.144;DP=217;Dels=0.00;FS=19.295;HaplotypeScore=2.3783;MLEAC=4;MLEAF=0.500;MQ=42.66;MQ0=22;MQRankSum=-5.472;QD=3.25;ReadPosRankSum=0.144 GT:AD:DP:GQ:PL 0/1:32,8:40:99:123,0,790 0/1:41,17:58:99:333,0,932 0/1:45,9:54:99:159,0,1133 0/1:54,11:65:99:123,0,1347 1 674456 . G A 153.90 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=0.702;DP=238;Dels=0.00;FS=8.086;HaplotypeScore=1.4249;MLEAC=2;MLEAF=0.250;MQ=40.98;MQ0=22;MQRankSum=-4.204;QD=1.37;ReadPosRankSum=-1.786 GT:AD:DP:GQ:PL 0/1:34,10:44:99:148,0,901 0/0:62,6:68:65:0,65,1527 0/0:55,3:58:91:0,91,1526 0/1:57,11:68:40:40,0,1496 1 675146 . G A 914.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.102;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.2167;MLEAC=8;MLEAF=1.00;MQ=15.31;MQ0=29;MQRankSum=1.575;QD=12.36;ReadPosRankSum=0.945 GT:AD:DP:GQ:PL 1/1:3,12:15:24:210,24,0 1/1:6,16:22:30:267,30,0 1/1:5,16:22:24:203,24,0 1/1:3,12:15:30:260,30,0 1 679604 . C A 631.44 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=226;Dels=0.00;FS=0.000;HaplotypeScore=0.2367;MLEAC=8;MLEAF=1.00;MQ=8.39;MQ0=197;QD=2.79 GT:AD:DP:GQ:PL 1/1:15,30:46:15:148,15,0 1/1:27,33:60:24:214,24,0 1/1:22,28:50:15:127,15,0 1/1:30,40:70:18:168,18,0 1 679692 . C T 68.12 HARD_TO_VALIDATE AC=3;AF=0.750;AN=4;BaseQRankSum=0.000;DP=26;Dels=0.00;FS=6.990;HaplotypeScore=0.2892;MLEAC=3;MLEAF=0.750;MQ=11.80;MQ0=17;MQRankSum=0.000;QD=4.87;ReadPosRankSum=-0.720 GT:AD:DP:GQ:PL 1/1:3,4:7:9:73,9,0 ./. 0/1:4,3:7:19:23,0,19 ./. 1 684862 . G A 146.38 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.059;DP=167;Dels=0.00;FS=0.000;HaplotypeScore=0.1835;MLEAC=3;MLEAF=0.375;MQ=7.74;MQ0=151;MQRankSum=0.953;QD=1.20;ReadPosRankSum=-1.694 GT:AD:DP:GQ:PL 0/0:32,13:45:6:0,6,53 0/1:29,13:42:51:51,0,51 0/1:29,14:43:74:74,0,79 0/1:23,14:37:23:54,0,23 1 694877 . A C 298.27 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=11.83;MQ0=34;QD=6.21 GT:AD:DP:GQ:PL 1/1:8,4:12:12:117,12,0 1/1:10,4:14:9:89,9,0 1/1:7,3:10:3:29,3,0 1/1:7,5:12:9:88,9,0 1 701236 . C T 75.44 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=2.578;DP=208;Dels=0.00;FS=3.388;HaplotypeScore=1.2569;MLEAC=2;MLEAF=0.250;MQ=20.87;MQ0=66;MQRankSum=-1.990;QD=0.74;ReadPosRankSum=2.229 GT:AD:DP:GQ:PL 0/1:37,6:43:35:35,0,446 0/0:48,2:50:54:0,54,707 0/0:51,5:56:1:0,1,787 0/1:48,11:59:72:72,0,871 1 701270 . A C 160.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.339;DP=198;Dels=0.00;FS=0.000;HaplotypeScore=0.4567;MLEAC=4;MLEAF=0.500;MQ=15.96;MQ0=107;MQRankSum=-1.743;QD=0.81;ReadPosRankSum=0.005 GT:AD:DP:GQ:PL 0/1:40,5:45:29:29,0,320 0/1:41,6:47:30:30,0,292 0/1:45,12:57:47:47,0,542 0/1:41,8:49:87:87,0,440 1 701946 . A G 455.77 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=22.36;MQ0=6;QD=16.88 GT:AD:DP:GQ:PL 1/1:0,6:6:15:153,15,0 1/1:0,9:9:12:121,12,0 1/1:0,2:2:6:59,6,0 1/1:0,10:10:15:148,15,0 1 702614 . A G 93.62 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=2.284;DP=142;Dels=0.00;FS=45.828;HaplotypeScore=1.1606;MLEAC=2;MLEAF=0.250;MQ=23.11;MQ0=23;MQRankSum=-3.472;QD=1.30;ReadPosRankSum=0.421 GT:AD:DP:GQ:PL 0/1:31,4:36:10:10,0,609 0/0:33,3:36:55:0,55,706 0/0:30,4:34:24:0,24,589 0/1:26,10:36:99:117,0,456 1 704367 . T C 434.68 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=25.56;MQ0=5;QD=16.10 GT:AD:DP:GQ:PL 1/1:0,4:4:9:78,9,0 1/1:0,11:11:18:167,18,0 1/1:0,6:6:15:136,15,0 1/1:0,6:6:9:79,9,0 1 706368 . A G 3076.35 PASS AC=8;AF=1.00;AN=8;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=1.0088;MLEAC=8;MLEAF=1.00;MQ=40.65;MQ0=4;QD=25.85 GT:AD:DP:GQ:PL 1/1:0,32:32:72:730,72,0 1/1:0,35:35:99:983,102,0 1/1:0,15:15:42:408,42,0 1/1:1,36:37:99:981,102,0 1 706778 . G A 2259.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=151;Dels=0.00;FS=0.000;HaplotypeScore=0.2416;MLEAC=8;MLEAF=1.00;MQ=21.80;MQ0=73;QD=14.96 GT:AD:DP:GQ:PL 1/1:16,19:35:54:549,54,0 1/1:18,28:47:75:714,75,0 1/1:11,21:32:45:442,45,0 1/1:16,21:37:60:580,60,0 1 708091 . A G 199.68 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.488;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=16.63;MQ0=9;MQRankSum=-0.992;QD=8.68;ReadPosRankSum=-1.736 GT:AD:DP:GQ:PL 1/1:0,5:5:3:26,3,0 1/1:1,4:5:6:59,6,0 1/1:0,6:6:9:79,9,0 1/1:0,7:7:6:60,6,0 1 713442 . T C 74.25 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.131;DP=122;Dels=0.00;FS=40.021;HaplotypeScore=1.4421;MLEAC=3;MLEAF=0.375;MQ=48.23;MQ0=4;MQRankSum=-6.297;QD=0.86;ReadPosRankSum=-4.276 GT:AD:DP:GQ:PL 0/1:24,7:31:46:46,0,665 0/1:22,4:26:47:47,0,626 0/1:24,5:29:15:15,0,717 0/0:29,7:36:15:0,15,871 1 714427 . G A 3373.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.699;DP=108;Dels=0.00;FS=0.000;HaplotypeScore=0.5567;MLEAC=8;MLEAF=1.00;MQ=40.64;MQ0=2;MQRankSum=-1.732;QD=31.23;ReadPosRankSum=0.544 GT:AD:DP:GQ:PL 1/1:2,25:28:72:800,72,0 1/1:0,27:27:78:848,78,0 1/1:0,24:24:72:812,72,0 1/1:0,29:29:87:939,87,0 1 715348 . T G 3762.35 PASS AC=8;AF=1.00;AN=8;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=0.7625;MLEAC=8;MLEAF=1.00;MQ=48.55;MQ0=0;QD=32.43 GT:AD:DP:GQ:PL 1/1:0,26:26:72:825,72,0 1/1:0,26:27:78:857,78,0 1/1:0,31:31:90:1014,90,0 1/1:0,32:32:96:1092,96,0 1 715996 . A T 1883.57 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=0.366;DP=104;Dels=0.00;FS=9.218;HaplotypeScore=1.6757;MLEAC=7;MLEAF=0.875;MQ=28.09;MQ0=31;MQRankSum=-0.423;QD=18.11;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL 0/1:2,29:31:6:463,0,6 1/1:1,19:20:9:368,9,0 1/1:0,23:23:45:472,45,0 1/1:0,30:30:57:609,57,0 1 718386 . A G 2127.35 PASS AC=8;AF=1.00;AN=8;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=33.56;MQ0=9;QD=21.71 GT:AD:DP:GQ:PL 1/1:0,18:18:39:370,39,0 1/1:0,42:42:99:993,108,0 1/1:0,17:17:33:302,33,0 1/1:0,21:21:54:488,54,0 1 718555 . T C 2941.35 PASS AC=8;AF=1.00;AN=8;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=0.7480;MLEAC=8;MLEAF=1.00;MQ=45.57;MQ0=1;QD=28.28 GT:AD:DP:GQ:PL 1/1:1,31:32:87:935,87,0 1/1:0,30:30:87:873,87,0 1/1:0,21:21:51:534,51,0 1/1:0,21:21:60:625,60,0 1 720240 . T C 2785.35 PASS AC=8;AF=1.00;AN=8;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=0.1835;MLEAC=8;MLEAF=1.00;MQ=35.18;MQ0=7;QD=27.58 GT:AD:DP:GQ:PL 1/1:0,21:21:48:521,48,0 1/1:0,31:31:81:901,81,0 1/1:0,22:22:51:578,51,0 1/1:0,27:27:72:811,72,0 1 720797 . G A 2208.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=0.4984;MLEAC=8;MLEAF=1.00;MQ=30.85;MQ0=14;QD=23.49 GT:AD:DP:GQ:PL 1/1:0,18:19:36:412,36,0 1/1:0,30:30:69:774,69,0 1/1:0,20:20:42:452,42,0 1/1:0,25:25:54:596,54,0 1 723891 . G C 3628.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.647;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=2.2234;MLEAC=8;MLEAF=1.00;MQ=48.41;MQ0=1;MQRankSum=1.391;QD=29.50;ReadPosRankSum=-0.426 GT:AD:DP:GQ:PL 1/1:2,28:30:72:750,72,0 1/1:0,35:35:99:1044,99,0 1/1:0,28:28:84:917,84,0 1/1:0,30:30:87:943,87,0 1 724189 . G A 77.14 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.284;DP=803;Dels=0.00;FS=7.187;HaplotypeScore=40.5266;MLEAC=2;MLEAF=0.250;MQ=28.83;MQ0=351;MQRankSum=2.117;QD=0.21;ReadPosRankSum=-3.949 GT:AD:DP:GQ:PL 0/1:208,7:219:15:15,0,1499 0/0:236,3:242:80:0,80,1486 0/1:135,10:148:96:96,0,1218 0/0:188,3:193:99:0,199,2457 1 724452 . C G 237.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.016;DP=298;Dels=0.00;FS=10.852;HaplotypeScore=6.2074;MLEAC=3;MLEAF=0.375;MQ=50.84;MQ0=30;MQRankSum=-6.950;QD=1.02;ReadPosRankSum=-4.428 GT:AD:DP:GQ:PL 0/0:57,8:65:28:0,28,1474 0/1:77,13:90:76:76,0,1910 0/1:60,10:70:48:48,0,1485 0/1:62,11:73:99:148,0,1591 1 724468 . G A 769.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.126;DP=414;Dels=0.00;FS=66.149;HaplotypeScore=15.6992;MLEAC=4;MLEAF=0.500;MQ=43.84;MQ0=74;MQRankSum=-8.796;QD=1.86;ReadPosRankSum=0.671 GT:AD:DP:GQ:PL 0/1:78,24:102:99:167,0,1443 0/1:85,25:110:99:160,0,1794 0/1:74,21:96:99:122,0,1582 0/1:76,30:106:99:353,0,1435 1 724469 . A T 117.92 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.732;DP=427;Dels=0.00;FS=18.603;HaplotypeScore=15.6865;MLEAC=3;MLEAF=0.375;MQ=43.13;MQ0=75;MQRankSum=-3.920;QD=0.36;ReadPosRankSum=4.049 GT:AD:DP:GQ:PL 0/0:95,7:103:99:0,114,1875 0/1:102,13:115:55:55,0,1910 0/1:88,10:98:23:23,0,1679 0/1:100,10:110:74:74,0,1810 1 724474 . A C 60.35 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-4.064;DP=473;Dels=0.00;FS=19.048;HaplotypeScore=21.6100;MLEAC=3;MLEAF=0.375;MQ=41.40;MQ0=84;MQRankSum=-2.972;QD=0.17;ReadPosRankSum=5.534 GT:AD:DP:GQ:PL 0/0:106,6:113:99:0,136,2060 0/1:113,13:126:22:22,0,1944 0/1:102,10:112:10:10,0,1823 0/1:111,10:122:62:62,0,1867 1 724475 . T A 137.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.759;DP=477;Dels=0.00;FS=21.882;HaplotypeScore=22.1092;MLEAC=3;MLEAF=0.375;MQ=41.09;MQ0=85;MQRankSum=-2.874;QD=0.38;ReadPosRankSum=5.748 GT:AD:DP:GQ:PL 0/0:101,11:112:72:0,72,1910 0/1:116,14:130:52:52,0,1993 0/1:98,14:112:49:49,0,1761 0/1:110,13:123:71:71,0,1896 1 724500 . C T 73.12 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=6.973;DP=384;Dels=0.00;FS=0.000;HaplotypeScore=33.6643;MLEAC=2;MLEAF=0.250;MQ=44.74;MQ0=54;MQRankSum=-9.354;QD=0.39;ReadPosRankSum=-0.020 GT:AD:DP:GQ:PL 0/1:67,13:87:25:25,0,1333 0/0:76,20:103:5:0,5,1645 0/0:67,22:92:77:0,77,1551 0/1:76,24:102:81:81,0,1386 1 724506 . G T 160.97 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=2.648;DP=474;Dels=0.01;FS=15.756;HaplotypeScore=39.5086;MLEAC=3;MLEAF=0.375;MQ=40.59;MQ0=91;MQRankSum=-4.162;QD=0.43;ReadPosRankSum=4.224 GT:AD:DP:GQ:PL 0/0:86,8:97:76:0,76,1783 0/1:103,11:117:66:66,0,1752 0/1:110,11:123:18:18,0,1817 0/1:114,16:133:99:111,0,1762 1 724621 . C G 48.98 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-1.140;DP=261;Dels=0.05;FS=62.652;HaplotypeScore=35.7074;MLEAC=2;MLEAF=0.250;MQ=33.85;MQ0=49;MQRankSum=-7.729;QD=0.37;ReadPosRankSum=1.650 GT:AD:DP:GQ:PL 0/0:51,9:63:96:0,96,1320 0/1:40,16:61:63:63,0,853 0/1:38,20:64:20:20,0,725 0/0:47,8:60:33:0,33,1064 1 724622 . A G 99 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=0.715;DP=267;Dels=0.04;FS=38.621;HaplotypeScore=36.4808;MLEAC=2;MLEAF=0.250;MQ=33.79;MQ0=50;MQRankSum=-7.330;QD=0.73;ReadPosRankSum=1.954 GT:AD:DP:GQ:PL 0/0:55,10:65:59:0,59,1297 0/1:48,14:63:19:19,0,938 0/1:40,24:65:99:114,0,748 0/0:50,11:61:71:0,71,1198 1 724637 . G A 66.83 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.060;DP=617;Dels=0.00;FS=81.596;HaplotypeScore=52.2720;MLEAC=3;MLEAF=0.375;MQ=26.50;MQ0=153;MQRankSum=-2.242;QD=0.14;ReadPosRankSum=0.775 GT:AD:DP:GQ:PL 0/0:104,11:124:99:0,141,1827 0/1:158,16:184:12:12,0,2042 0/1:113,18:135:80:80,0,1319 0/1:154,15:174:8:8,0,1916 1 724642 . G A 210.94 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=8.472;DP=642;Dels=0.00;FS=92.306;HaplotypeScore=70.2990;MLEAC=3;MLEAF=0.375;MQ=25.48;MQ0=170;MQRankSum=-0.623;QD=0.45;ReadPosRankSum=4.356 GT:AD:DP:GQ:PL 0/1:110,14:125:21:21,0,1470 0/1:168,30:199:99:173,0,1931 0/1:125,15:142:51:51,0,1295 0/0:166,10:176:68:0,68,1914 1 724652 . C T 823.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.732;DP=667;Dels=0.00;FS=39.500;HaplotypeScore=88.9382;MLEAC=4;MLEAF=0.500;MQ=25.12;MQ0=176;MQRankSum=-4.328;QD=1.24;ReadPosRankSum=-8.407 GT:AD:DP:GQ:PL 0/1:85,30:125:99:291,0,1113 0/1:136,35:201:99:244,0,1836 0/1:110,29:155:99:133,0,1425 0/1:127,49:185:99:188,0,1727 1 724655 . T A 210.95 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-4.353;DP=677;Dels=0.00;FS=58.563;HaplotypeScore=76.7636;MLEAC=2;MLEAF=0.250;MQ=24.86;MQ0=181;MQRankSum=1.204;QD=0.64;ReadPosRankSum=3.490 GT:AD:DP:GQ:PL 0/1:107,11:126:50:50,0,1303 0/1:163,22:203:99:195,0,1869 0/0:146,9:162:20:0,20,1657 0/0:164,11:186:99:0,107,2175 1 724657 . G A 183.33 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.640;DP=676;Dels=0.00;FS=22.131;HaplotypeScore=73.1780;MLEAC=2;MLEAF=0.250;MQ=24.72;MQ0=185;MQRankSum=-2.864;QD=0.60;ReadPosRankSum=-6.350 GT:AD:DP:GQ:PL 0/1:104,20:124:99:202,0,1088 0/0:183,22:205:71:0,71,2326 0/0:147,16:163:2:0,2,1650 0/1:154,30:184:13:13,0,2018 1 724673 . A T 377.95 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.510;DP=657;Dels=0.00;FS=75.894;HaplotypeScore=49.0740;MLEAC=4;MLEAF=0.500;MQ=26.27;MQ0=185;MQRankSum=-1.122;QD=0.58;ReadPosRankSum=2.502 GT:AD:DP:GQ:PL 0/1:108,13:124:27:27,0,1301 0/1:170,30:203:99:145,0,2202 0/1:127,24:153:99:210,0,1413 0/1:147,25:177:28:28,0,1903 1 724696 . A T 74.93 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=3.783;DP=329;Dels=0.00;FS=47.944;HaplotypeScore=34.0239;MLEAC=2;MLEAF=0.250;MQ=33.86;MQ0=67;MQRankSum=-4.329;QD=0.46;ReadPosRankSum=0.673 GT:AD:DP:GQ:PL 0/0:60,4:70:39:0,39,1186 0/0:60,11:94:31:0,31,1308 0/1:55,9:76:25:25,0,1006 0/1:64,13:88:84:84,0,1273 1 724830 . A T 422.95 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.433;DP=136;Dels=0.00;FS=103.975;HaplotypeScore=2.6302;MLEAC=4;MLEAF=0.500;MQ=46.13;MQ0=10;MQRankSum=-8.339;QD=3.11;ReadPosRankSum=-5.799 GT:AD:DP:GQ:PL 0/1:27,12:39:29:29,0,814 0/1:21,16:37:99:252,0,569 0/1:17,10:28:68:68,0,457 0/1:20,12:32:99:106,0,558 1 724836 . T G 434.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.960;DP=161;Dels=0.00;FS=104.283;HaplotypeScore=4.2218;MLEAC=4;MLEAF=0.500;MQ=40.73;MQ0=28;MQRankSum=-6.761;QD=2.70;ReadPosRankSum=-1.426 GT:AD:DP:GQ:PL 0/1:28,12:40:45:45,0,681 0/1:27,16:43:99:250,0,543 0/1:24,13:37:68:68,0,457 0/1:29,12:41:99:104,0,542 1 724837 . G A 387.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-1.585;DP=174;Dels=0.00;FS=97.023;HaplotypeScore=4.0051;MLEAC=4;MLEAF=0.500;MQ=39.06;MQ0=34;MQRankSum=-5.718;QD=2.23;ReadPosRankSum=-0.248 GT:AD:DP:GQ:PL 0/1:31,12:43:30:30,0,711 0/1:27,16:43:99:223,0,541 0/1:31,10:41:66:66,0,433 0/1:35,12:47:99:101,0,572 1 724869 . C A 800.96 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.268;DP=98;Dels=0.00;FS=54.326;HaplotypeScore=9.9308;MLEAC=4;MLEAF=0.500;MQ=36.18;MQ0=22;MQRankSum=5.139;QD=8.17;ReadPosRankSum=0.132 GT:AD:DP:GQ:PL 0/1:8,12:20:23:359,0,23 0/1:22,7:29:99:185,0,173 0/1:13,8:21:99:169,0,125 0/1:22,6:28:99:120,0,301 1 724871 . C G 727.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.290;DP=97;Dels=0.00;FS=61.154;HaplotypeScore=9.6850;MLEAC=4;MLEAF=0.500;MQ=35.37;MQ0=22;MQRankSum=4.673;QD=7.50;ReadPosRankSum=-0.582 GT:AD:DP:GQ:PL 0/1:9,10:19:62:301,0,62 0/1:23,7:30:99:192,0,208 0/1:14,6:20:99:142,0,127 0/1:20,6:28:99:125,0,311 1 724873 . A C 66.46 HARD_TO_VALIDATE AC=1;AF=0.125;AN=8;BaseQRankSum=-3.047;DP=100;Dels=0.00;FS=20.885;HaplotypeScore=5.2746;MLEAC=1;MLEAF=0.125;MQ=35.79;MQ0=22;MQRankSum=-0.197;QD=2.22;ReadPosRankSum=-0.553 GT:AD:DP:GQ:PL 0/0:20,0:20:42:0,42,482 0/0:29,1:30:13:0,13,420 0/0:20,0:20:30:0,30,327 0/1:25,5:30:98:98,0,384 1 724928 . A T 102.58 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.226;DP=194;Dels=0.00;FS=46.560;HaplotypeScore=14.3356;MLEAC=4;MLEAF=0.500;MQ=30.42;MQ0=41;MQRankSum=-1.890;QD=0.53;ReadPosRankSum=2.871 GT:AD:DP:GQ:PL 0/1:39,6:46:50:50,0,623 0/1:46,6:53:12:12,0,555 0/1:25,5:32:2:2,0,447 0/1:49,12:63:69:69,0,855 1 724931 . T G 112.12 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.367;DP=217;Dels=0.00;FS=49.098;HaplotypeScore=11.9297;MLEAC=4;MLEAF=0.500;MQ=30.52;MQ0=45;MQRankSum=-3.872;QD=0.52;ReadPosRankSum=1.807 GT:AD:DP:GQ:PL 0/1:38,8:52:44:44,0,716 0/1:38,16:61:12:12,0,610 0/1:23,9:36:27:27,0,441 0/1:51,15:68:61:61,0,927 1 724948 . T A 412.45 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=4.383;DP=481;Dels=0.00;FS=26.325;HaplotypeScore=120.9025;MLEAC=3;MLEAF=0.375;MQ=23.45;MQ0=174;MQRankSum=-1.371;QD=0.86;ReadPosRankSum=-2.968 GT:AD:DP:GQ:PL 0/1:71,24:105:38:38,0,589 0/1:85,39:130:99:218,0,750 0/1:72,28:106:99:108,0,681 0/1:96,38:140:99:116,0,841 1 724972 . A G 54.91 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.543;DP=639;Dels=0.00;FS=6.136;HaplotypeScore=99.7438;MLEAC=2;MLEAF=0.250;MQ=25.50;MQ0=217;MQRankSum=-2.643;QD=0.18;ReadPosRankSum=-0.419 GT:AD:DP:GQ:PL 0/0:118,11:137:99:0,138,1467 0/0:167,17:196:69:0,69,1628 0/1:131,14:155:32:32,0,1270 0/1:122,15:151:57:57,0,896 1 724979 . C A 100.45 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=0.451;DP=567;Dels=0.01;FS=0.000;HaplotypeScore=101.1796;MLEAC=1;MLEAF=0.125;MQ=28.01;MQ0=176;MQRankSum=-5.151;QD=0.76;ReadPosRankSum=7.155 GT:AD:DP:GQ:PL 0/0:99,14:122:40:0,40,1287 0/0:126,23:165:22:0,22,1647 0/0:104,23:141:3:0,3,1456 0/1:84,34:131:99:131,0,793 1 724981 . A C 118.33 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-3.046;DP=574;Dels=0.01;FS=1.318;HaplotypeScore=97.5375;MLEAC=1;MLEAF=0.125;MQ=28.18;MQ0=175;MQRankSum=-4.106;QD=0.97;ReadPosRankSum=4.643 GT:AD:DP:GQ:PL 0/1:79,25:122:99:150,0,1030 0/0:121,26:165:99:0,102,1891 0/0:109,21:144:35:0,35,1509 0/0:95,20:135:78:0,78,1084 1 725022 . T G 415 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.523;DP=282;Dels=0.02;FS=10.837;HaplotypeScore=53.7479;MLEAC=4;MLEAF=0.500;MQ=42.66;MQ0=35;MQRankSum=-7.535;QD=1.47;ReadPosRankSum=0.455 GT:AD:DP:GQ:PL 0/1:36,20:60:99:163,0,696 0/1:58,18:80:99:170,0,1253 0/1:59,20:84:17:17,0,1482 0/1:35,16:52:97:97,0,761 1 725026 . T C 264.93 HARD_TO_VALIDATE AC=2;AF=0.250;AN=8;BaseQRankSum=-1.816;DP=271;Dels=0.02;FS=0.807;HaplotypeScore=67.7715;MLEAC=2;MLEAF=0.250;MQ=43.70;MQ0=28;MQRankSum=-7.950;QD=1.91;ReadPosRankSum=-1.799 GT:AD:DP:GQ:PL 0/1:43,11:56:99:126,0,827 0/0:62,15:79:59:0,59,1544 0/1:56,23:80:99:173,0,1480 0/0:42,9:51:22:0,22,964 1 725040 . C T 396.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=7.294;DP=395;Dels=0.03;FS=19.945;HaplotypeScore=79.9945;MLEAC=3;MLEAF=0.375;MQ=39.08;MQ0=51;MQRankSum=-7.297;QD=1.45;ReadPosRankSum=-3.329 GT:AD:DP:GQ:PL 0/1:52,16:73:99:112,0,1053 0/0:91,26:120:31:0,31,1819 0/1:82,17:100:99:106,0,1819 0/1:59,30:92:99:213,0,1021 1 725046 . T G 223.75 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.562;DP=543;Dels=0.00;FS=1.019;HaplotypeScore=80.3520;MLEAC=3;MLEAF=0.375;MQ=34.71;MQ0=102;MQRankSum=-4.929;QD=0.54;ReadPosRankSum=-2.126 GT:AD:DP:GQ:PL 0/1:85,22:109:19:19,0,1411 0/1:136,27:167:76:76,0,2384 0/0:109,21:131:9:0,9,2272 0/1:100,32:135:99:162,0,1621 1 725071 . G T 99.33 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=1.554;DP=993;Dels=0.00;FS=8.241;HaplotypeScore=92.3319;MLEAC=1;MLEAF=0.125;MQ=23.64;MQ0=304;MQRankSum=0.068;QD=0.40;ReadPosRankSum=-1.452 GT:AD:DP:GQ:PL 0/0:225,15:249:99:0,206,2673 0/0:224,11:244:99:0,145,2261 0/1:222,22:250:99:131,0,2096 0/0:220,21:250:75:0,75,2546 1 725086 . G C 53.57 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-5.738;DP=997;Dels=0.00;FS=2.669;HaplotypeScore=133.1976;MLEAC=1;MLEAF=0.125;MQ=21.70;MQ0=329;MQRankSum=0.562;QD=0.21;ReadPosRankSum=1.420 GT:AD:DP:GQ:PL 0/0:236,5:248:99:0,211,2673 0/0:227,13:249:99:0,144,2182 0/1:223,21:250:85:85,0,1852 0/0:223,19:250:10:0,10,2019 1 725114 . A T 98.97 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.533;DP=994;Dels=0.00;FS=30.358;HaplotypeScore=115.3605;MLEAC=2;MLEAF=0.250;MQ=21.35;MQ0=325;MQRankSum=0.180;QD=0.20;ReadPosRankSum=-4.402 GT:AD:DP:GQ:PL 0/0:237,10:248:28:0,28,2154 0/1:226,20:247:8:8,0,2090 0/1:228,18:249:99:124,0,2179 0/0:228,18:250:43:0,43,2267 1 725126 . G T 33.34 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=0.089;DP=817;Dels=0.01;FS=79.446;HaplotypeScore=160.8698;MLEAC=1;MLEAF=0.125;MQ=22.71;MQ0=238;MQRankSum=1.974;QD=0.17;ReadPosRankSum=0.098 GT:AD:DP:GQ:PL 0/0:176,5:196:37:0,37,1888 0/0:194,7:218:33:0,33,1735 0/1:180,10:200:65:65,0,2064 0/0:172,8:197:48:0,48,1861 1 725127 . A G 2048.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.362;DP=767;Dels=0.02;FS=133.910;HaplotypeScore=185.2120;MLEAC=4;MLEAF=0.500;MQ=23.35;MQ0=212;MQRankSum=-1.894;QD=2.67;ReadPosRankSum=-0.895 GT:AD:DP:GQ:PL 0/1:112,58:185:99:668,0,1050 0/1:122,66:197:99:664,0,1179 0/1:127,48:185:99:498,0,1514 0/1:116,47:181:99:251,0,1564 1 725130 . T A 38.35 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-2.996;DP=732;Dels=0.05;FS=20.348;HaplotypeScore=178.7335;MLEAC=1;MLEAF=0.125;MQ=23.69;MQ0=193;MQRankSum=-3.604;QD=0.22;ReadPosRankSum=1.169 GT:AD:DP:GQ:PL 0/0:141,28:172:21:0,21,1859 0/0:159,22:183:91:0,91,2056 0/1:152,20:174:70:70,0,2049 0/0:148,20:169:80:0,80,1916 1 725132 . C G 1887.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-6.150;DP=735;Dels=0.02;FS=24.806;HaplotypeScore=184.7278;MLEAC=4;MLEAF=0.500;MQ=23.74;MQ0=195;MQRankSum=-6.161;QD=2.57;ReadPosRankSum=3.590 GT:AD:DP:GQ:PL 0/1:84,73:176:99:562,0,1062 0/1:89,85:196:99:601,0,1128 0/1:91,69:172:99:539,0,1411 0/1:102,60:175:99:218,0,1365 1 725145 . T A 208.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.418;DP=878;Dels=0.00;FS=12.992;HaplotypeScore=113.2956;MLEAC=3;MLEAF=0.375;MQ=23.10;MQ0=255;MQRankSum=-0.871;QD=0.32;ReadPosRankSum=4.834 GT:AD:DP:GQ:PL 0/1:195,20:216:26:26,0,2149 0/1:199,25:224:99:128,0,2179 0/1:183,21:205:89:89,0,2231 0/0:212,17:230:53:0,53,2247 1 725150 . T G 276.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-4.260;DP=721;Dels=0.00;FS=2.199;HaplotypeScore=103.5960;MLEAC=3;MLEAF=0.375;MQ=24.14;MQ0=209;MQRankSum=-2.620;QD=0.52;ReadPosRankSum=3.842 GT:AD:DP:GQ:PL 0/1:142,24:177:34:34,0,1809 0/1:162,27:196:85:85,0,1979 0/1:126,29:159:99:192,0,1686 0/0:160,19:188:40:0,40,1906 1 725155 . T A 96.19 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.162;DP=708;Dels=0.00;FS=2.246;HaplotypeScore=104.5786;MLEAC=2;MLEAF=0.250;MQ=24.30;MQ0=204;MQRankSum=-4.596;QD=0.27;ReadPosRankSum=3.607 GT:AD:DP:GQ:PL 0/0:145,17:170:12:0,12,1823 0/1:141,26:193:71:71,0,1859 0/1:124,21:157:59:59,0,1735 0/0:141,21:185:23:0,23,1712 1 725156 . A G 2380.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.853;DP=704;Dels=0.00;FS=23.585;HaplotypeScore=92.3189;MLEAC=4;MLEAF=0.500;MQ=24.40;MQ0=204;MQRankSum=-5.666;QD=3.38;ReadPosRankSum=6.019 GT:AD:DP:GQ:PL 0/1:86,78:167:99:655,0,1154 0/1:111,79:193:99:748,0,1316 0/1:89,64:158:99:635,0,1229 0/1:120,65:186:99:375,0,1438 1 725175 . A T 146.39 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.606;DP=370;Dels=0.00;FS=21.549;HaplotypeScore=57.1141;MLEAC=4;MLEAF=0.500;MQ=31.87;MQ0=75;MQRankSum=-6.327;QD=0.40;ReadPosRankSum=-3.756 GT:AD:DP:GQ:PL 0/1:58,18:81:57:57,0,1197 0/1:72,17:99:32:32,0,1330 0/1:75,18:99:86:86,0,1389 0/1:72,15:90:2:2,0,1291 1 725176 . G T 344.97 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.708;DP=327;Dels=0.00;FS=34.423;HaplotypeScore=60.7658;MLEAC=4;MLEAF=0.500;MQ=33.74;MQ0=53;MQRankSum=-7.467;QD=1.05;ReadPosRankSum=-0.717 GT:AD:DP:GQ:PL 0/1:52,8:72:20:20,0,1256 0/1:54,21:89:79:79,0,1185 0/1:52,17:87:99:151,0,1168 0/1:54,16:79:99:127,0,1173 1 725188 . G A 451.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.794;DP=295;Dels=0.02;FS=37.232;HaplotypeScore=39.0034;MLEAC=4;MLEAF=0.500;MQ=36.01;MQ0=54;MQRankSum=-10.782;QD=1.53;ReadPosRankSum=-2.369 GT:AD:DP:GQ:PL 0/1:47,16:63:99:117,0,1034 0/1:52,26:78:52:52,0,1140 0/1:43,30:73:99:219,0,1164 0/1:45,28:75:96:96,0,976 1 725199 . G A 40.79 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=-0.434;DP=289;Dels=0.00;FS=29.543;HaplotypeScore=24.3136;MLEAC=3;MLEAF=0.375;MQ=37.82;MQ0=55;MQRankSum=-8.717;QD=0.19;ReadPosRankSum=-0.155 GT:AD:DP:GQ:PL 0/1:56,15:71:28:28,0,1252 0/1:59,18:77:17:17,0,1227 0/0:54,17:72:9:0,9,1377 0/1:51,18:69:29:29,0,975 1 725316 . G A 324.03 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.964;DP=798;Dels=0.00;FS=4.707;HaplotypeScore=45.8820;MLEAC=3;MLEAF=0.375;MQ=31.14;MQ0=215;MQRankSum=-0.968;QD=0.53;ReadPosRankSum=-2.387 GT:AD:DP:GQ:PL 0/1:165,23:193:99:154,0,1643 0/1:193,23:219:99:200,0,2225 0/0:160,18:184:48:0,48,1818 0/1:178,18:202:2:2,0,2346 1 725356 . G T 534.47 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=2.998;DP=407;Dels=0.00;FS=8.883;HaplotypeScore=40.0059;MLEAC=4;MLEAF=0.500;MQ=40.72;MQ0=81;MQRankSum=-5.999;QD=1.74;ReadPosRankSum=10.397 GT:AD:DP:GQ:PL 0/1:67,19:90:99:231,0,1015 0/1:90,21:111:99:253,0,1731 0/0:83,15:99:1:0,1,1381 0/1:88,16:107:81:81,0,1671 1 725536 . G A 488.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.958;DP=985;Dels=0.00;FS=60.171;HaplotypeScore=102.5397;MLEAC=4;MLEAF=0.500;MQ=24.77;MQ0=373;MQRankSum=-0.258;QD=0.50;ReadPosRankSum=-5.301 GT:AD:DP:GQ:PL 0/1:213,19:245:67:67,0,1762 0/1:211,19:241:95:95,0,1572 0/1:216,27:249:99:100,0,1889 0/1:211,30:250:99:259,0,1951 1 725550 . T G 80.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=5.476;DP=999;Dels=0.00;FS=10.859;HaplotypeScore=126.8457;MLEAC=2;MLEAF=0.250;MQ=26.58;MQ0=278;MQRankSum=-0.186;QD=0.16;ReadPosRankSum=-5.324 GT:AD:DP:GQ:PL 0/1:223,23:250:39:39,0,2405 0/1:222,23:249:76:76,0,2034 0/0:231,13:250:71:0,71,2343 0/0:241,7:249:99:0,260,3555 1 725556 . A G 4076.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.740;DP=910;Dels=0.00;FS=57.760;HaplotypeScore=201.0686;MLEAC=4;MLEAF=0.500;MQ=27.92;MQ0=221;MQRankSum=-5.968;QD=4.48;ReadPosRankSum=-10.523 GT:AD:DP:GQ:PL 0/1:124,71:218:99:704,0,1601 0/1:97,108:231:99:1157,0,876 0/1:108,95:221:99:789,0,1223 0/1:117,108:237:99:1459,0,1462 1 725559 . C T 146.17 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.816;DP=914;Dels=0.01;FS=19.450;HaplotypeScore=263.6645;MLEAC=3;MLEAF=0.375;MQ=28.70;MQ0=164;MQRankSum=1.355;QD=0.21;ReadPosRankSum=-3.723 GT:AD:DP:GQ:PL 0/1:186,17:215:29:29,0,2499 0/1:222,15:245:12:12,0,2673 0/0:187,12:206:43:0,43,2252 0/1:206,22:241:99:139,0,3072 1 725566 . G A 808.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-4.460;DP=942;Dels=0.02;FS=20.365;HaplotypeScore=261.1380;MLEAC=4;MLEAF=0.500;MQ=28.81;MQ0=155;MQRankSum=0.474;QD=0.86;ReadPosRankSum=-2.013 GT:AD:DP:GQ:PL 0/1:189,23:214:99:162,0,2634 0/1:218,27:245:99:246,0,2510 0/1:189,24:214:99:106,0,2431 0/1:212,32:245:99:327,0,3412 1 725569 . T A 2078.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-3.486;DP=954;Dels=0.02;FS=25.177;HaplotypeScore=215.5667;MLEAC=4;MLEAF=0.500;MQ=28.61;MQ0=154;MQRankSum=-7.272;QD=2.18;ReadPosRankSum=1.024 GT:AD:DP:GQ:PL 0/1:139,68:226:99:424,0,2256 0/1:136,92:247:99:619,0,1945 0/1:123,78:220:99:380,0,2098 0/1:157,73:244:99:688,0,2821 1 725582 . G A 1356.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.392;DP=998;Dels=0.00;FS=29.615;HaplotypeScore=187.0722;MLEAC=4;MLEAF=0.500;MQ=26.81;MQ0=189;MQRankSum=2.577;QD=1.36;ReadPosRankSum=1.042 GT:AD:DP:GQ:PL 0/1:207,41:249:99:565,0,2727 0/1:216,24:249:99:189,0,2605 0/1:217,23:250:99:192,0,2436 0/1:209,33:249:99:443,0,2769 1 725587 . G A 32.98 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=7.085;DP=999;Dels=0.02;FS=2.388;HaplotypeScore=165.7905;MLEAC=2;MLEAF=0.250;MQ=25.81;MQ0=210;MQRankSum=-1.237;QD=0.07;ReadPosRankSum=1.806 GT:AD:DP:GQ:PL 0/1:223,24:247:22:22,0,2895 0/0:216,24:245:22:0,22,2231 0/0:229,16:245:44:0,44,2292 0/1:224,20:246:45:45,0,2397 1 725591 . G A 341.97 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.108;DP=999;Dels=0.01;FS=8.067;HaplotypeScore=154.6432;MLEAC=3;MLEAF=0.375;MQ=25.45;MQ0=218;MQRankSum=-4.814;QD=0.46;ReadPosRankSum=5.964 GT:AD:DP:GQ:PL 0/1:209,39:249:18:18,0,3291 0/1:197,48:245:99:219,0,2219 0/0:210,32:247:99:0,123,2859 0/1:199,46:247:99:139,0,2709 1 725600 . T A 536.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.064;DP=992;Dels=0.00;FS=3.094;HaplotypeScore=140.2967;MLEAC=4;MLEAF=0.500;MQ=25.19;MQ0=236;MQRankSum=0.967;QD=0.54;ReadPosRankSum=-0.632 GT:AD:DP:GQ:PL 0/1:200,31:249:99:189,0,2877 0/1:204,26:247:99:113,0,2265 0/1:196,29:242:99:162,0,2397 0/1:210,27:247:99:105,0,2633 1 725606 . T C 91.49 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-6.372;DP=967;Dels=0.01;FS=12.262;HaplotypeScore=175.6321;MLEAC=2;MLEAF=0.250;MQ=25.48;MQ0=228;MQRankSum=-3.411;QD=0.19;ReadPosRankSum=1.915 GT:AD:DP:GQ:PL 0/0:201,34:247:73:0,73,3255 0/0:204,31:243:30:0,30,2603 0/1:176,34:224:6:6,0,2695 0/1:201,38:244:99:118,0,2850 1 725611 . G A 163.96 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.624;DP=989;Dels=0.01;FS=4.438;HaplotypeScore=185.3910;MLEAC=3;MLEAF=0.375;MQ=25.07;MQ0=253;MQRankSum=2.845;QD=0.22;ReadPosRankSum=2.093 GT:AD:DP:GQ:PL 0/1:226,19:246:99:104,0,2985 0/1:230,18:248:19:19,0,2580 0/1:222,16:238:75:75,0,2726 0/0:235,12:248:49:0,49,3026 1 725615 . C T 122.44 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=6.287;DP=989;Dels=0.01;FS=32.877;HaplotypeScore=193.3785;MLEAC=2;MLEAF=0.250;MQ=25.15;MQ0=251;MQRankSum=-1.324;QD=0.25;ReadPosRankSum=0.033 GT:AD:DP:GQ:PL 0/1:201,32:246:99:119,0,2585 0/0:224,19:248:1:0,1,2364 0/0:210,20:240:99:0,127,2811 0/1:221,22:246:35:35,0,2715 1 725623 . A G 31.92 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=0.336;DP=999;Dels=0.00;FS=35.494;HaplotypeScore=210.7126;MLEAC=2;MLEAF=0.250;MQ=25.12;MQ0=253;MQRankSum=2.306;QD=0.06;ReadPosRankSum=-1.566 GT:AD:DP:GQ:PL 0/0:235,15:250:80:0,80,3488 0/0:238,11:249:99:0,133,2850 0/1:234,16:250:27:27,0,3059 0/1:231,18:249:39:39,0,3016 1 725630 . T A 129.66 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.308;DP=965;Dels=0.03;FS=15.460;HaplotypeScore=160.7210;MLEAC=3;MLEAF=0.375;MQ=25.00;MQ0=251;MQRankSum=-2.293;QD=0.18;ReadPosRankSum=1.230 GT:AD:DP:GQ:PL 0/1:207,27:234:46:46,0,3207 0/1:205,24:229:99:112,0,2428 0/1:206,25:231:4:4,0,2816 0/0:220,26:246:13:0,13,3003 1 725632 . A T 126.96 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-3.174;DP=946;Dels=0.03;FS=16.748;HaplotypeScore=167.4271;MLEAC=2;MLEAF=0.250;MQ=25.05;MQ0=244;MQRankSum=-2.638;QD=0.27;ReadPosRankSum=6.855 GT:AD:DP:GQ:PL 0/1:186,20:227:36:36,0,2847 0/0:179,25:220:59:0,59,2585 0/1:168,32:223:99:125,0,2340 0/0:203,30:247:19:0,19,2959 1 725635 . T A 358.01 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.583;DP=961;Dels=0.00;FS=25.464;HaplotypeScore=190.2925;MLEAC=3;MLEAF=0.375;MQ=24.89;MQ0=244;MQRankSum=-0.920;QD=0.49;ReadPosRankSum=-1.286 GT:AD:DP:GQ:PL 0/1:193,42:241:99:320,0,2782 0/1:212,26:246:56:56,0,2734 0/0:209,13:228:99:0,131,3016 0/1:210,28:246:16:16,0,2983 1 725642 . G T 130.03 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.760;DP=952;Dels=0.00;FS=37.450;HaplotypeScore=205.9782;MLEAC=2;MLEAF=0.250;MQ=25.43;MQ0=245;MQRankSum=2.202;QD=0.28;ReadPosRankSum=6.467 GT:AD:DP:GQ:PL 0/0:213,17:244:2:0,2,3005 0/0:222,9:243:99:0,141,2905 0/1:188,18:219:99:118,0,2477 0/1:217,19:246:44:44,0,2960 1 725647 . C A 83.14 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-0.323;DP=950;Dels=0.00;FS=66.672;HaplotypeScore=139.2986;MLEAC=2;MLEAF=0.250;MQ=26.06;MQ0=246;MQRankSum=-6.092;QD=0.17;ReadPosRankSum=0.989 GT:AD:DP:GQ:PL 0/1:186,39:239:99:102,0,3030 0/1:187,44:247:15:15,0,2762 0/0:184,21:215:99:0,191,3068 0/0:202,43:249:99:0,106,3267 1 725657 . T C 76.38 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-0.947;DP=918;Dels=0.00;FS=11.737;HaplotypeScore=99.0192;MLEAC=1;MLEAF=0.125;MQ=26.49;MQ0=244;MQRankSum=0.128;QD=0.32;ReadPosRankSum=0.278 GT:AD:DP:GQ:PL 0/0:216,10:233:99:0,118,3108 0/0:231,8:242:99:0,109,3023 0/0:190,10:207:17:0,17,2634 0/1:212,19:236:99:108,0,2923 1 725667 . G T 281.96 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.507;DP=860;Dels=0.00;FS=1.431;HaplotypeScore=106.1032;MLEAC=4;MLEAF=0.500;MQ=27.34;MQ0=224;MQRankSum=1.086;QD=0.33;ReadPosRankSum=-0.073 GT:AD:DP:GQ:PL 0/1:200,20:220:99:181,0,2629 0/1:218,16:235:26:26,0,2824 0/1:169,14:185:84:84,0,2282 0/1:205,15:220:23:23,0,2978 1 725669 . C T 192.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=3.841;DP=836;Dels=0.00;FS=24.105;HaplotypeScore=87.8459;MLEAC=2;MLEAF=0.250;MQ=27.44;MQ0=221;MQRankSum=-0.840;QD=0.49;ReadPosRankSum=-0.112 GT:AD:DP:GQ:PL 0/0:181,24:218:87:0,87,2922 0/0:185,17:227:99:0,125,2887 0/1:141,27:176:58:58,0,2134 0/1:172,29:214:99:169,0,2607 1 725684 . C A 385.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.953;DP=431;Dels=0.03;FS=0.000;HaplotypeScore=54.5776;MLEAC=3;MLEAF=0.375;MQ=33.60;MQ0=93;MQRankSum=-8.132;QD=1.12;ReadPosRankSum=-5.139 GT:AD:DP:GQ:PL 0/1:75,18:93:99:123,0,1200 0/1:98,20:119:38:38,0,1796 0/0:70,15:85:99:0,110,1536 0/1:79,39:118:99:259,0,1718 1 725686 . T G 88.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=4.989;DP=400;Dels=0.02;FS=0.000;HaplotypeScore=49.5494;MLEAC=2;MLEAF=0.250;MQ=34.74;MQ0=77;MQRankSum=-6.691;QD=0.43;ReadPosRankSum=-4.651 GT:AD:DP:GQ:PL 0/1:64,13:83:62:62,0,1283 0/0:92,12:111:50:0,50,1988 0/0:69,8:81:99:0,104,1468 0/1:82,23:116:61:61,0,1817 1 725705 . G A 31.34 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-1.625;DP=279;Dels=0.00;FS=32.938;HaplotypeScore=19.1643;MLEAC=1;MLEAF=0.125;MQ=40.40;MQ0=45;MQRankSum=-3.618;QD=0.55;ReadPosRankSum=-1.433 GT:AD:DP:GQ:PL 0/1:42,9:57:63:63,0,919 0/0:70,4:79:99:0,102,1714 0/0:66,2:73:99:0,109,1493 0/0:61,6:70:99:0,110,1606 1 725765 . T A 248.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.978;DP=536;Dels=0.01;FS=28.583;HaplotypeScore=44.9815;MLEAC=3;MLEAF=0.375;MQ=35.07;MQ0=94;MQRankSum=-4.627;QD=0.61;ReadPosRankSum=-2.651 GT:AD:DP:GQ:PL 0/1:118,16:134:36:36,0,1699 0/1:108,26:134:99:151,0,1878 0/0:101,21:124:33:0,33,1934 0/1:110,27:137:96:96,0,1996 1 725777 . G C 120.33 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-2.384;DP=726;Dels=0.00;FS=26.112;HaplotypeScore=110.8354;MLEAC=1;MLEAF=0.125;MQ=33.21;MQ0=139;MQRankSum=-0.558;QD=0.64;ReadPosRankSum=0.549 GT:AD:DP:GQ:PL 0/0:146,12:175:93:0,93,2354 0/1:150,20:188:99:152,0,2159 0/0:142,7:168:81:0,81,2144 0/0:168,6:194:99:0,153,2620 1 725784 . A T 30.36 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-2.007;DP=758;Dels=0.01;FS=56.426;HaplotypeScore=158.1739;MLEAC=1;MLEAF=0.125;MQ=33.35;MQ0=144;MQRankSum=-3.084;QD=0.17;ReadPosRankSum=2.684 GT:AD:DP:GQ:PL 0/0:159,16:177:99:0,147,2576 0/0:190,11:201:99:0,138,3170 0/1:155,18:173:62:62,0,2289 0/0:181,20:202:21:0,21,2877 1 725785 . G T 186.61 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.972;DP=748;Dels=0.01;FS=10.761;HaplotypeScore=164.9744;MLEAC=2;MLEAF=0.250;MQ=33.62;MQ0=136;MQRankSum=-9.700;QD=0.32;ReadPosRankSum=-3.719 GT:AD:DP:GQ:PL 0/1:107,51:171:99:202,0,1791 0/1:122,56:199:99:134,0,2415 0/0:118,40:172:1:0,1,2238 0/1:146,39:201:16:16,0,2674 1 725807 . C G 50.33 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-2.287;DP=985;Dels=0.00;FS=1.438;HaplotypeScore=121.5251;MLEAC=1;MLEAF=0.125;MQ=28.43;MQ0=225;MQRankSum=-2.053;QD=0.21;ReadPosRankSum=-2.431 GT:AD:DP:GQ:PL 0/0:221,14:248:99:0,160,3253 0/0:204,29:249:62:0,62,2593 0/1:199,25:241:82:82,0,2395 0/0:207,24:246:90:0,90,2879 1 725810 . T G 49.33 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=2.932;DP=998;Dels=0.00;FS=29.585;HaplotypeScore=131.9978;MLEAC=1;MLEAF=0.125;MQ=28.13;MQ0=233;MQRankSum=1.246;QD=0.20;ReadPosRankSum=1.563 GT:AD:DP:GQ:PL 0/0:221,16:249:98:0,98,3100 0/1:218,19:249:81:81,0,2543 0/0:226,16:250:47:0,47,2732 0/0:223,12:249:99:0,115,3064 1 725822 . G A 2376.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=11.052;DP=951;Dels=0.00;FS=30.006;HaplotypeScore=110.7683;MLEAC=4;MLEAF=0.500;MQ=28.68;MQ0=211;MQRankSum=-2.037;QD=2.50;ReadPosRankSum=3.837 GT:AD:DP:GQ:PL 0/1:171,56:235:99:607,0,2211 0/1:161,65:238:99:670,0,1685 0/1:166,71:240:99:754,0,1777 0/1:184,51:238:99:378,0,2102 1 725841 . T G 458.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.173;DP=773;Dels=0.02;FS=1.876;HaplotypeScore=170.5990;MLEAC=3;MLEAF=0.375;MQ=33.31;MQ0=121;MQRankSum=-3.667;QD=0.80;ReadPosRankSum=5.561 GT:AD:DP:GQ:PL 0/1:154,27:181:99:109,0,2709 0/0:161,29:190:99:0,117,2727 0/1:146,35:181:99:234,0,2447 0/1:173,32:205:99:150,0,2696 1 725855 . T A 415.42 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.602;DP=754;Dels=0.00;FS=21.180;HaplotypeScore=188.6320;MLEAC=3;MLEAF=0.375;MQ=35.96;MQ0=101;MQRankSum=-2.494;QD=0.74;ReadPosRankSum=0.404 GT:AD:DP:GQ:PL 0/0:173,21:196:11:0,11,3412 0/1:161,25:187:99:295,0,2590 0/1:156,17:174:50:50,0,2779 0/1:175,22:197:99:104,0,3064 1 725861 . G T 2773.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.021;DP=744;Dels=0.00;FS=2.187;HaplotypeScore=103.8430;MLEAC=4;MLEAF=0.500;MQ=36.83;MQ0=95;MQRankSum=-5.576;QD=3.73;ReadPosRankSum=-6.650 GT:AD:DP:GQ:PL 0/1:124,67:192:99:888,0,2527 0/1:123,57:183:99:809,0,2181 0/1:132,37:171:99:417,0,2381 0/1:142,54:198:99:692,0,2565 1 725872 . G A 59.35 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=6.460;DP=691;Dels=0.00;FS=40.014;HaplotypeScore=113.1679;MLEAC=1;MLEAF=0.125;MQ=39.32;MQ0=72;MQRankSum=-3.842;QD=0.34;ReadPosRankSum=2.126 GT:AD:DP:GQ:PL 0/1:153,21:175:89:89,0,2888 0/0:150,15:167:0:0,0,2647 0/0:140,8:150:99:0,164,2682 0/0:174,20:196:18:0,18,3289 1 725879 . T A 962.96 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.804;DP=739;Dels=0.00;FS=14.515;HaplotypeScore=207.9247;MLEAC=4;MLEAF=0.500;MQ=39.90;MQ0=75;MQRankSum=-10.696;QD=1.30;ReadPosRankSum=-2.684 GT:AD:DP:GQ:PL 0/1:126,42:185:99:248,0,3003 0/1:140,39:187:22:22,0,3212 0/1:108,38:155:99:176,0,2408 0/1:149,54:211:99:549,0,3120 1 725883 . A G 6443.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.916;DP=810;Dels=0.00;FS=5.347;HaplotypeScore=221.6868;MLEAC=4;MLEAF=0.500;MQ=38.73;MQ0=93;MQRankSum=-3.411;QD=7.96;ReadPosRankSum=5.609 GT:AD:DP:GQ:PL 0/1:110,98:208:99:2062,0,1782 0/1:119,86:205:99:1857,0,1698 0/1:117,55:172:99:1045,0,1889 0/1:134,91:225:99:1512,0,2639 1 725886 . G A 1026.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.253;DP=893;Dels=0.00;FS=2.059;HaplotypeScore=223.8795;MLEAC=4;MLEAF=0.500;MQ=38.75;MQ0=95;MQRankSum=-3.423;QD=1.15;ReadPosRankSum=4.490 GT:AD:DP:GQ:PL 0/1:205,31:237:99:144,0,4278 0/1:185,31:216:99:149,0,3575 0/1:154,35:190:99:375,0,2967 0/1:211,39:250:99:391,0,4172 1 725889 . A G 325.92 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.443;DP=903;Dels=0.00;FS=2.832;HaplotypeScore=217.0350;MLEAC=2;MLEAF=0.250;MQ=39.03;MQ0=88;MQRankSum=-4.448;QD=0.72;ReadPosRankSum=3.820 GT:AD:DP:GQ:PL 0/1:204,33:239:99:133,0,4402 0/1:190,24:214:99:227,0,3615 0/0:183,14:197:74:0,74,3711 0/0:227,23:250:24:0,24,4626 1 725894 . A G 5256.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.260;DP=941;Dels=0.00;FS=6.206;HaplotypeScore=219.4077;MLEAC=4;MLEAF=0.500;MQ=38.20;MQ0=92;MQRankSum=-2.872;QD=5.59;ReadPosRankSum=5.911 GT:AD:DP:GQ:PL 0/1:160,88:248:99:1692,0,2902 0/1:161,72:233:99:1409,0,2705 0/1:163,47:210:99:886,0,2844 0/1:172,77:250:99:1302,0,3304 1 725903 . T A 10656.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=5.641;DP=945;Dels=0.04;FS=12.428;HaplotypeScore=242.2666;MLEAC=4;MLEAF=0.500;MQ=37.15;MQ0=96;MQRankSum=-15.561;QD=11.28;ReadPosRankSum=-1.275 GT:AD:DP:GQ:PL 0/1:61,169:231:99:3080,0,894 0/1:77,149:229:99:2323,0,1378 0/1:70,137:212:99:2390,0,1386 0/1:69,167:237:99:2896,0,1288 1 725905 . T A 149.69 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.479;DP=979;Dels=0.03;FS=0.000;HaplotypeScore=175.2614;MLEAC=3;MLEAF=0.375;MQ=34.40;MQ0=127;MQRankSum=-5.950;QD=0.20;ReadPosRankSum=0.502 GT:AD:DP:GQ:PL 0/1:210,31:241:7:7,0,4015 0/0:203,23:227:99:0,226,3626 0/1:200,37:237:99:141,0,3795 0/1:210,34:244:35:35,0,4073 1 725937 . G C 786.96 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=3.679;DP=994;Dels=0.01;FS=0.789;HaplotypeScore=248.1717;MLEAC=4;MLEAF=0.500;MQ=26.11;MQ0=277;MQRankSum=0.319;QD=0.79;ReadPosRankSum=2.743 GT:AD:DP:GQ:PL 0/1:207,30:247:99:305,0,2250 0/1:201,30:247:99:286,0,1737 0/1:208,25:246:99:204,0,2275 0/1:202,29:246:24:24,0,2252 1 725944 . C A 3448.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.666;DP=968;Dels=0.02;FS=5.923;HaplotypeScore=208.0441;MLEAC=4;MLEAF=0.500;MQ=26.51;MQ0=264;MQRankSum=-2.605;QD=3.56;ReadPosRankSum=3.101 GT:AD:DP:GQ:PL 0/1:143,76:238:99:869,0,1482 0/1:133,82:242:99:813,0,1234 0/1:141,76:236:99:911,0,1593 0/1:127,92:236:99:888,0,1357 1 725946 . G A 55.82 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.136;DP=985;Dels=0.01;FS=74.304;HaplotypeScore=210.5399;MLEAC=2;MLEAF=0.250;MQ=26.46;MQ0=261;MQRankSum=0.554;QD=0.11;ReadPosRankSum=-2.747 GT:AD:DP:GQ:PL 0/1:200,16:242:83:83,0,2517 0/0:209,11:247:99:0,167,2508 0/0:203,16:241:96:0,96,2724 0/1:205,11:246:5:5,0,2244 1 725947 . C G 95.42 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.319;DP=998;Dels=0.01;FS=1.987;HaplotypeScore=207.0876;MLEAC=3;MLEAF=0.375;MQ=26.69;MQ0=266;MQRankSum=-2.496;QD=0.13;ReadPosRankSum=2.485 GT:AD:DP:GQ:PL 0/1:211,28:247:9:9,0,2799 0/1:219,20:248:63:63,0,2123 0/1:212,27:245:57:57,0,2676 0/0:217,20:247:99:0,118,2693 1 725952 . G C 45.96 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=4.045;DP=993;Dels=0.00;FS=45.193;HaplotypeScore=187.9693;MLEAC=2;MLEAF=0.250;MQ=26.58;MQ0=248;MQRankSum=1.962;QD=0.09;ReadPosRankSum=-0.265 GT:AD:DP:GQ:PL 0/1:229,15:248:59:59,0,2776 0/0:234,7:244:99:0,160,2511 0/0:234,14:250:99:0,108,2809 0/1:237,10:249:21:21,0,2456 1 725962 . A G 494.45 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-5.443;DP=855;Dels=0.00;FS=7.188;HaplotypeScore=120.6639;MLEAC=4;MLEAF=0.500;MQ=28.65;MQ0=170;MQRankSum=-4.576;QD=0.58;ReadPosRankSum=0.028 GT:AD:DP:GQ:PL 0/1:167,41:219:99:198,0,2618 0/1:167,38:212:7:7,0,2079 0/1:152,46:206:99:128,0,2188 0/1:167,38:218:99:193,0,2103 1 725977 . G T 161.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.352;DP=671;Dels=0.01;FS=1.373;HaplotypeScore=152.7010;MLEAC=3;MLEAF=0.375;MQ=31.44;MQ0=107;MQRankSum=-2.578;QD=0.33;ReadPosRankSum=3.847 GT:AD:DP:GQ:PL 0/1:141,16:160:51:51,0,2109 0/1:125,21:151:28:28,0,1847 0/1:147,23:174:99:117,0,2214 0/0:147,30:179:49:0,49,2303 1 725980 . C T 3854.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.293;DP=592;Dels=0.04;FS=0.717;HaplotypeScore=152.9680;MLEAC=4;MLEAF=0.500;MQ=32.98;MQ0=84;MQRankSum=-12.024;QD=6.51;ReadPosRankSum=2.709 GT:AD:DP:GQ:PL 0/1:50,78:129:99:993,0,897 0/1:45,85:132:99:861,0,875 0/1:51,93:150:99:879,0,1122 0/1:46,113:159:99:1154,0,942 1 725987 . G A 387.93 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=5.364;DP=656;Dels=0.00;FS=0.000;HaplotypeScore=178.4872;MLEAC=3;MLEAF=0.375;MQ=32.19;MQ0=98;MQRankSum=-1.387;QD=0.76;ReadPosRankSum=1.177 GT:AD:DP:GQ:PL 0/0:132,15:148:24:0,24,2150 0/1:134,24:158:99:209,0,1686 0/1:145,23:169:76:76,0,2059 0/1:155,26:181:99:137,0,2090 1 725994 . A G 225.91 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=0.087;DP=690;Dels=0.00;FS=9.454;HaplotypeScore=118.1401;MLEAC=2;MLEAF=0.250;MQ=31.99;MQ0=111;MQRankSum=-1.169;QD=0.63;ReadPosRankSum=0.846 GT:AD:DP:GQ:PL 0/0:149,7:156:99:0,148,2656 0/1:147,21:168:99:224,0,1850 0/0:163,12:176:80:0,80,2511 0/1:172,17:190:36:36,0,2322 1 725996 . T G 151.92 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.772;DP=684;Dels=0.00;FS=0.000;HaplotypeScore=99.4945;MLEAC=3;MLEAF=0.375;MQ=32.17;MQ0=107;MQRankSum=-3.530;QD=0.29;ReadPosRankSum=-5.780 GT:AD:DP:GQ:PL 0/1:113,25:158:99:124,0,1982 0/0:138,18:164:31:0,31,1981 0/1:141,22:174:32:32,0,2235 0/1:151,29:188:30:30,0,2204 1 726009 . C T 141 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.548;DP=672;Dels=0.01;FS=4.143;HaplotypeScore=101.9743;MLEAC=2;MLEAF=0.250;MQ=33.88;MQ0=93;MQRankSum=-2.361;QD=0.40;ReadPosRankSum=6.461 GT:AD:DP:GQ:PL 0/0:135,7:152:99:0,120,2444 0/1:134,19:162:99:156,0,2050 0/0:141,11:163:72:0,72,2413 0/1:166,17:186:19:19,0,2404 1 726010 . C T 731.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.643;DP=657;Dels=0.01;FS=13.749;HaplotypeScore=100.3025;MLEAC=4;MLEAF=0.500;MQ=34.19;MQ0=90;MQRankSum=-3.971;QD=1.11;ReadPosRankSum=-3.636 GT:AD:DP:GQ:PL 0/1:108,35:152:99:272,0,1886 0/1:116,32:154:99:187,0,1980 0/1:126,28:161:99:187,0,2148 0/1:145,28:181:99:118,0,2213 1 726016 . G A 87.94 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.243;DP=739;Dels=0.00;FS=11.366;HaplotypeScore=108.1977;MLEAC=2;MLEAF=0.250;MQ=33.28;MQ0=107;MQRankSum=-1.366;QD=0.25;ReadPosRankSum=-3.653 GT:AD:DP:GQ:PL 0/1:147,19:166:37:37,0,2401 0/1:166,18:184:85:85,0,2385 0/0:171,6:177:99:0,170,2865 0/0:194,16:211:21:0,21,2849 1 726029 . C A 731.90 HARD_TO_VALIDATE AC=3;AF=0.375;AN=8;BaseQRankSum=-1.205;DP=604;Dels=0.01;FS=3.219;HaplotypeScore=114.2410;MLEAC=3;MLEAF=0.375;MQ=36.09;MQ0=64;MQRankSum=-6.772;QD=1.61;ReadPosRankSum=2.771 GT:AD:DP:GQ:PL 0/0:121,23:147:63:0,63,2316 0/1:110,37:151:99:386,0,2061 0/1:105,24:132:75:75,0,2204 0/1:129,36:166:99:305,0,2189 1 726031 . G T 194.88 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.881;DP=608;Dels=0.01;FS=8.867;HaplotypeScore=117.0005;MLEAC=3;MLEAF=0.375;MQ=36.27;MQ0=64;MQRankSum=-3.188;QD=0.41;ReadPosRankSum=3.189 GT:AD:DP:GQ:PL 0/1:122,20:146:99:130,0,2208 0/1:127,18:150:92:92,0,2290 0/0:119,7:129:99:0,113,2539 0/1:153,18:176:6:6,0,2703 1 726064 . A G 216.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-4.032;DP=807;Dels=0.00;FS=52.530;HaplotypeScore=82.4313;MLEAC=2;MLEAF=0.250;MQ=33.21;MQ0=157;MQRankSum=-1.592;QD=0.53;ReadPosRankSum=-0.983 GT:AD:DP:GQ:PL 0/0:195,14:210:43:0,43,3013 0/1:178,19:199:99:185,0,2386 0/0:167,13:184:57:0,57,2974 0/1:186,25:214:66:66,0,3149 1 726066 . G A 405.90 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=4.817;DP=812;Dels=0.00;FS=13.692;HaplotypeScore=74.5183;MLEAC=3;MLEAF=0.375;MQ=33.40;MQ0=155;MQRankSum=-2.185;QD=0.65;ReadPosRankSum=3.902 GT:AD:DP:GQ:PL 0/1:187,25:212:99:168,0,2799 0/1:177,23:201:99:143,0,2503 0/0:168,17:185:99:0,110,3103 0/1:190,23:214:99:129,0,3063 1 726082 . G C 242.37 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.903;DP=663;Dels=0.00;FS=56.198;HaplotypeScore=36.3378;MLEAC=3;MLEAF=0.375;MQ=36.29;MQ0=102;MQRankSum=-3.667;QD=0.47;ReadPosRankSum=4.571 GT:AD:DP:GQ:PL 0/1:164,17:181:4:4,0,2872 0/1:142,18:160:99:170,0,2218 0/0:132,14:147:28:0,28,2737 0/1:146,29:175:99:101,0,2874 1 726099 . A T 56.33 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=0.837;DP=640;Dels=0.03;FS=9.441;HaplotypeScore=88.9434;MLEAC=1;MLEAF=0.125;MQ=38.07;MQ0=70;MQRankSum=-2.927;QD=0.34;ReadPosRankSum=-0.536 GT:AD:DP:GQ:PL 0/0:143,16:159:46:0,46,2838 0/1:142,18:160:88:88,0,2440 0/0:126,11:137:41:0,41,2753 0/0:149,12:162:34:0,34,2905 1 726100 . A G 76.45 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=0.351;DP=636;Dels=0.03;FS=10.857;HaplotypeScore=101.7480;MLEAC=1;MLEAF=0.125;MQ=37.95;MQ0=70;MQRankSum=-2.891;QD=0.47;ReadPosRankSum=-0.602 GT:AD:DP:GQ:PL 0/0:139,18:157:14:0,14,2739 0/1:141,18:159:99:108,0,2424 0/0:130,10:140:57:0,57,2858 0/0:148,12:160:21:0,21,2768 1 726107 . T G 3233.06 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-3.289;DP=590;Dels=0.01;FS=63.325;HaplotypeScore=117.7532;MLEAC=4;MLEAF=0.500;MQ=38.68;MQ0=69;MQRankSum=-9.445;QD=5.48;ReadPosRankSum=3.198 GT:AD:DP:GQ:PL 0/1:86,61:153:99:691,0,1863 0/1:91,57:151:99:895,0,1536 0/1:81,45:129:99:763,0,1807 0/1:83,64:149:99:917,0,1706 1 726110 . A T 162.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=0.310;DP=624;Dels=0.01;FS=4.076;HaplotypeScore=102.9881;MLEAC=2;MLEAF=0.250;MQ=37.73;MQ0=85;MQRankSum=-4.020;QD=0.54;ReadPosRankSum=2.463 GT:AD:DP:GQ:PL 0/1:138,18:158:75:75,0,2532 0/0:152,14:166:52:0,52,2603 0/1:119,17:137:99:122,0,2462 0/0:140,15:155:62:0,62,2609 1 726113 . C G 2176.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.135;DP=645;Dels=0.01;FS=30.015;HaplotypeScore=98.9326;MLEAC=4;MLEAF=0.500;MQ=37.09;MQ0=102;MQRankSum=-8.321;QD=3.38;ReadPosRankSum=1.219 GT:AD:DP:GQ:PL 0/1:120,44:165:99:358,0,2333 0/1:108,60:171:99:749,0,1771 0/1:93,45:138:99:519,0,1899 0/1:108,54:163:99:583,0,1937 1 726145 . C T 756.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.087;DP=950;Dels=0.00;FS=0.692;HaplotypeScore=111.5165;MLEAC=4;MLEAF=0.500;MQ=30.78;MQ0=180;MQRankSum=-7.851;QD=0.80;ReadPosRankSum=-9.110 GT:AD:DP:GQ:PL 0/1:180,52:235:99:291,0,2884 0/1:163,71:237:89:89,0,2368 0/1:195,40:237:66:66,0,2966 0/1:174,61:239:99:343,0,2479 1 726156 . T A 888.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-2.092;DP=967;Dels=0.01;FS=0.398;HaplotypeScore=147.1781;MLEAC=4;MLEAF=0.500;MQ=30.79;MQ0=165;MQRankSum=3.323;QD=0.92;ReadPosRankSum=8.872 GT:AD:DP:GQ:PL 0/1:210,29:239:99:300,0,3156 0/1:215,23:239:99:137,0,2601 0/1:215,25:240:99:183,0,2866 0/1:209,30:239:99:301,0,2540 1 726159 . C A 105.35 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-2.116;DP=936;Dels=0.01;FS=7.924;HaplotypeScore=144.5960;MLEAC=1;MLEAF=0.125;MQ=30.86;MQ0=154;MQRankSum=-4.992;QD=0.44;ReadPosRankSum=2.739 GT:AD:DP:GQ:PL 0/0:196,34:230:60:0,60,3544 0/1:197,35:235:99:137,0,2487 0/0:195,35:231:22:0,22,3002 0/0:197,30:229:99:0,156,3113 1 726173 . G A 322.35 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.204;DP=935;Dels=0.00;FS=0.544;HaplotypeScore=131.7537;MLEAC=2;MLEAF=0.250;MQ=30.22;MQ0=134;MQRankSum=3.256;QD=0.70;ReadPosRankSum=6.943 GT:AD:DP:GQ:PL 0/1:199,23:222:99:109,0,3363 0/0:215,19:241:10:0,10,2810 0/0:213,18:236:21:0,21,3297 0/1:205,27:236:99:247,0,2855 1 726178 . A G 270.92 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-4.917;DP=957;Dels=0.04;FS=3.302;HaplotypeScore=211.6951;MLEAC=2;MLEAF=0.250;MQ=30.46;MQ0=136;MQRankSum=-7.712;QD=0.56;ReadPosRankSum=9.060 GT:AD:DP:GQ:PL 0/0:181,41:226:34:0,34,3771 0/1:173,52:232:97:97,0,2538 0/0:179,42:226:26:0,26,3331 0/1:167,55:229:99:208,0,3027 1 726183 . C A 971.45 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.774;DP=941;Dels=0.00;FS=4.634;HaplotypeScore=200.3178;MLEAC=4;MLEAF=0.500;MQ=30.12;MQ0=135;MQRankSum=1.222;QD=1.03;ReadPosRankSum=-4.574 GT:AD:DP:GQ:PL 0/1:180,40:235:99:378,0,3290 0/1:185,29:239:7:7,0,2309 0/1:182,32:233:99:146,0,3074 0/1:165,40:232:99:472,0,2564 1 726185 . T A 5407.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.369;DP=949;Dels=0.01;FS=0.850;HaplotypeScore=190.0846;MLEAC=4;MLEAF=0.500;MQ=29.90;MQ0=141;MQRankSum=-13.059;QD=5.70;ReadPosRankSum=10.908 GT:AD:DP:GQ:PL 0/1:108,129:237:99:1276,0,2332 0/1:90,145:241:99:1138,0,1452 0/1:99,133:233:99:1179,0,2123 0/1:76,147:227:99:1847,0,1489 1 726203 . G T 99.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=6.357;DP=981;Dels=0.00;FS=5.796;HaplotypeScore=120.1611;MLEAC=2;MLEAF=0.250;MQ=27.06;MQ0=169;MQRankSum=0.102;QD=0.20;ReadPosRankSum=4.404 GT:AD:DP:GQ:PL 0/1:211,22:249:64:64,0,3321 0/0:208,17:245:89:0,89,2541 0/1:216,18:248:70:70,0,2599 0/0:212,8:239:99:0,128,3099 1 726205 . A T 154.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.882;DP=983;Dels=0.00;FS=3.934;HaplotypeScore=119.6273;MLEAC=2;MLEAF=0.250;MQ=26.73;MQ0=176;MQRankSum=-0.001;QD=0.31;ReadPosRankSum=4.938 GT:AD:DP:GQ:PL 0/1:210,21:250:95:95,0,3406 0/0:201,16:243:71:0,71,2507 0/1:216,19:250:94:94,0,2741 0/0:206,10:239:87:0,87,3088 1 726220 . C T 121.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-2.737;DP=816;Dels=0.02;FS=31.232;HaplotypeScore=124.0530;MLEAC=2;MLEAF=0.250;MQ=27.08;MQ0=176;MQRankSum=-2.192;QD=0.30;ReadPosRankSum=4.140 GT:AD:DP:GQ:PL 0/1:172,22:204:75:75,0,2750 0/0:169,24:201:99:0,103,2529 0/0:169,21:193:42:0,42,2305 0/1:172,18:199:81:81,0,2331 1 726235 . G T 184.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.216;DP=482;Dels=0.00;FS=2.428;HaplotypeScore=63.0348;MLEAC=3;MLEAF=0.375;MQ=30.97;MQ0=91;MQRankSum=-4.845;QD=0.50;ReadPosRankSum=1.672 GT:AD:DP:GQ:PL 0/1:98,14:121:30:30,0,1749 0/1:100,24:132:98:98,0,1744 0/0:93,17:115:61:0,61,1766 0/1:85,18:112:91:91,0,1594 1 726248 . A G 519.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-8.216;DP=372;Dels=0.00;FS=16.356;HaplotypeScore=33.5390;MLEAC=4;MLEAF=0.500;MQ=33.83;MQ0=50;MQRankSum=-10.339;QD=1.40;ReadPosRankSum=1.577 GT:AD:DP:GQ:PL 0/1:52,30:95:99:163,0,1415 0/1:59,25:99:99:130,0,1565 0/1:45,29:89:62:62,0,1261 0/1:47,31:89:99:197,0,1175 1 726481 . T G 5934.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.648;DP=219;Dels=0.00;FS=5.366;HaplotypeScore=1.7519;MLEAC=8;MLEAF=1.00;MQ=50.09;MQ0=20;MQRankSum=6.148;QD=27.10;ReadPosRankSum=4.828 GT:AD:DP:GQ:PL 1/1:10,55:65:99:1666,103,0 1/1:9,53:62:99:1706,124,0 1/1:2,47:49:99:1600,138,0 1/1:12,31:43:61:988,61,0 1 726564 . T C 205.88 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-8.278;DP=529;Dels=0.00;FS=0.000;HaplotypeScore=24.6222;MLEAC=3;MLEAF=0.375;MQ=34.23;MQ0=121;MQRankSum=-6.545;QD=0.51;ReadPosRankSum=-7.182 GT:AD:DP:GQ:PL 0/1:102,27:129:99:169,0,1554 0/1:105,28:133:64:64,0,1369 0/0:105,23:128:39:0,39,1992 0/1:102,36:138:6:6,0,1412 1 726601 . A G 632.73 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.227;DP=851;Dels=0.03;FS=1.276;HaplotypeScore=124.9361;MLEAC=4;MLEAF=0.500;MQ=22.45;MQ0=313;MQRankSum=-6.946;QD=0.74;ReadPosRankSum=-4.122 GT:AD:DP:GQ:PL 0/1:140,62:210:99:251,0,1369 0/1:149,45:202:5:5,0,1421 0/1:143,64:213:99:221,0,1431 0/1:122,65:198:99:187,0,1117 1 726728 . T A 121.89 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.838;DP=849;Dels=0.00;FS=7.147;HaplotypeScore=32.0945;MLEAC=3;MLEAF=0.375;MQ=29.60;MQ0=346;MQRankSum=-0.132;QD=0.19;ReadPosRankSum=-5.724 GT:AD:DP:GQ:PL 0/1:187,15:203:34:34,0,1684 0/1:214,15:230:50:50,0,1904 0/1:185,23:208:71:71,0,2014 0/0:194,11:208:8:0,8,1771 1 726733 . T C 181.68 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.428;DP=821;Dels=0.00;FS=8.692;HaplotypeScore=30.8261;MLEAC=3;MLEAF=0.375;MQ=29.66;MQ0=341;MQRankSum=0.039;QD=0.30;ReadPosRankSum=-5.248 GT:AD:DP:GQ:PL 0/1:184,9:194:82:82,0,1561 0/1:207,11:220:53:53,0,1836 0/1:183,13:199:79:79,0,1890 0/0:197,9:207:5:0,5,1707 1 726739 . G C 184.69 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-5.326;DP=720;Dels=0.00;FS=8.604;HaplotypeScore=29.8014;MLEAC=4;MLEAF=0.500;MQ=31.72;MQ0=272;MQRankSum=-0.954;QD=0.26;ReadPosRankSum=-3.460 GT:AD:DP:GQ:PL 0/1:154,12:167:78:78,0,1615 0/1:180,12:194:57:57,0,1830 0/1:158,13:172:79:79,0,1928 0/1:176,11:187:1:1,0,1685 1 726764 . G T 305.05 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=0.424;DP=294;Dels=0.00;FS=0.678;HaplotypeScore=15.1044;MLEAC=4;MLEAF=0.500;MQ=50.39;MQ0=25;MQRankSum=-7.299;QD=1.04;ReadPosRankSum=8.255 GT:AD:DP:GQ:PL 0/1:57,9:66:99:107,0,1433 0/1:69,11:80:93:93,0,1612 0/1:68,14:82:99:123,0,1642 0/1:59,7:66:14:14,0,1451 1 726767 . T A 335.99 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=1.810;DP=266;Dels=0.00;FS=0.000;HaplotypeScore=7.9346;MLEAC=4;MLEAF=0.500;MQ=52.28;MQ0=13;MQRankSum=-9.040;QD=1.26;ReadPosRankSum=8.610 GT:AD:DP:GQ:PL 0/1:42,9:56:99:119,0,1283 0/1:58,13:79:89:89,0,1597 0/1:53,13:71:99:142,0,1453 0/1:47,8:60:18:18,0,1323 1 726922 . C A 1664.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.552;DP=902;Dels=0.00;FS=17.669;HaplotypeScore=111.1723;MLEAC=4;MLEAF=0.500;MQ=19.33;MQ0=251;MQRankSum=-0.385;QD=1.85;ReadPosRankSum=-3.402 GT:AD:DP:GQ:PL 0/1:138,84:231:99:470,0,941 0/1:115,77:201:99:319,0,1084 0/1:152,82:245:99:547,0,1306 0/1:147,59:223:99:361,0,1240 1 726924 . T G 710.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.417;DP=921;Dels=0.00;FS=0.000;HaplotypeScore=117.1164;MLEAC=4;MLEAF=0.500;MQ=19.48;MQ0=269;MQRankSum=0.891;QD=0.77;ReadPosRankSum=-3.380 GT:AD:DP:GQ:PL 0/1:149,44:232:99:208,0,1231 0/1:144,34:200:99:128,0,1153 0/1:145,52:248:99:321,0,1318 0/1:159,43:237:86:86,0,1387 1 726942 . A C 35.33 HARD_TO_VALIDATE;LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-0.596;DP=960;Dels=0.00;FS=1.024;HaplotypeScore=97.3420;MLEAC=1;MLEAF=0.125;MQ=18.51;MQ0=321;MQRankSum=-0.104;QD=0.14;ReadPosRankSum=1.252 GT:AD:DP:GQ:PL 0/0:209,19:241:67:0,67,1548 0/0:202,14:221:43:0,43,1446 0/0:218,22:249:76:0,76,1759 0/1:211,19:249:67:67,0,1283 1 726944 . C G 1253.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=11.747;DP=968;Dels=0.00;FS=4.048;HaplotypeScore=97.7848;MLEAC=4;MLEAF=0.500;MQ=17.93;MQ0=329;MQRankSum=-1.461;QD=1.30;ReadPosRankSum=5.717 GT:AD:DP:GQ:PL 0/1:145,71:241:99:492,0,443 0/1:161,44:230:99:367,0,569 0/1:174,56:248:99:278,0,870 0/1:174,57:249:99:149,0,890 1 727004 . C A 115.33 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=6.917;DP=928;Dels=0.00;FS=8.253;HaplotypeScore=97.7309;MLEAC=1;MLEAF=0.125;MQ=23.46;MQ0=346;MQRankSum=3.090;QD=0.51;ReadPosRankSum=-2.804 GT:AD:DP:GQ:PL 0/0:213,5:236:99:0,141,1851 0/1:207,13:228:99:147,0,1409 0/0:207,10:236:35:0,35,1401 0/0:198,8:227:73:0,73,1295 1 727018 . A T 43.93 HARD_TO_VALIDATE;LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-2.437;DP=768;Dels=0.01;FS=5.600;HaplotypeScore=51.8242;MLEAC=2;MLEAF=0.250;MQ=27.48;MQ0=253;MQRankSum=-3.527;QD=0.11;ReadPosRankSum=3.092 GT:AD:DP:GQ:PL 0/1:172,22:198:24:24,0,1843 0/0:170,24:197:99:0,178,2176 0/1:159,23:182:54:54,0,1799 0/0:155,24:185:99:0,135,1756 1 727024 . G A 78.33 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=3.007;DP=678;Dels=0.00;FS=12.696;HaplotypeScore=47.0993;MLEAC=1;MLEAF=0.125;MQ=29.06;MQ0=214;MQRankSum=2.377;QD=0.47;ReadPosRankSum=4.690 GT:AD:DP:GQ:PL 0/0:181,3:184:99:0,142,2088 0/1:151,11:166:99:110,0,1635 0/0:160,6:168:69:0,69,1923 0/0:156,3:160:99:0,99,1525 1 727030 . A G 105.34 HARD_TO_VALIDATE;LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-1.831;DP=431;Dels=0.00;FS=18.155;HaplotypeScore=22.3123;MLEAC=1;MLEAF=0.125;MQ=35.60;MQ0=103;MQRankSum=-2.602;QD=0.96;ReadPosRankSum=4.512 GT:AD:DP:GQ:PL 0/0:101,9:112:50:0,50,1608 0/1:94,14:110:99:137,0,1377 0/0:93,10:103:47:0,47,1680 0/0:92,12:106:30:0,30,1299 1 728159 . C T 2177.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=108;Dels=0.00;FS=0.000;HaplotypeScore=0.2493;MLEAC=8;MLEAF=1.00;MQ=26.81;MQ0=24;QD=20.16 GT:AD:DP:GQ:PL 1/1:0,28:28:48:506,48,0 1/1:0,28:28:57:596,57,0 1/1:0,21:21:39:431,39,0 1/1:0,30:30:63:670,63,0 1 728242 . C G 2871.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=127;Dels=0.00;FS=0.000;HaplotypeScore=0.1663;MLEAC=8;MLEAF=1.00;MQ=27.81;MQ0=21;QD=22.61 GT:AD:DP:GQ:PL 1/1:0,28:28:54:560,54,0 1/1:0,27:27:63:645,63,0 1/1:0,37:37:75:830,75,0 1/1:0,35:35:84:862,84,0 1 729679 . C G 4789.35 PASS AC=8;AF=1.00;AN=8;DP=153;Dels=0.00;FS=0.000;HaplotypeScore=0.9931;MLEAC=8;MLEAF=1.00;MQ=47.73;MQ0=0;QD=31.30 GT:AD:DP:GQ:PL 1/1:1,37:38:99:1125,99,0 1/1:0,40:40:99:1306,117,0 1/1:0,34:34:99:1111,102,0 1/1:0,41:41:99:1273,114,0 1 730825 . C T 1678.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.903;DP=126;Dels=0.00;FS=2.276;HaplotypeScore=0.6022;MLEAC=4;MLEAF=0.500;MQ=38.06;MQ0=1;MQRankSum=0.032;QD=13.32;ReadPosRankSum=1.422 GT:AD:DP:GQ:PL 0/1:13,13:26:99:265,0,329 0/1:9,18:27:99:522,0,224 0/1:19,15:34:99:390,0,528 0/1:19,20:39:99:534,0,485 1 733998 . C T 373.08 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=18.62;MQ0=14;QD=12.44 GT:AD:DP:GQ:PL ./. 1/1:0,14:14:18:181,18,0 1/1:0,2:2:3:30,3,0 1/1:0,14:14:18:187,18,0 1 734042 . G A 1374.38 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.6972;MLEAC=8;MLEAF=1.00;MQ=32.70;MQ0=12;QD=22.17 GT:AD:DP:GQ:PL 1/1:0,10:10:18:208,18,0 1/1:0,18:18:33:363,33,0 1/1:0,12:12:24:271,24,0 1/1:0,22:22:51:558,51,0 1 734462 . G A 1095.37 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.5887;MLEAC=8;MLEAF=1.00;MQ=31.45;MQ0=11;QD=23.31 GT:AD:DP:GQ:PL 1/1:1,13:14:24:262,24,0 1/1:2,10:12:27:302,27,0 1/1:0,13:13:30:322,30,0 1/1:0,8:8:21:235,21,0 1 734491 . T C 466.20 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.576;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=21.13;MQ0=14;MQRankSum=1.103;QD=12.95;ReadPosRankSum=1.103 GT:AD:DP:GQ:PL 1/1:1,9:10:3:23,3,0 1/1:0,11:11:18:182,18,0 1/1:0,11:11:21:220,21,0 1/1:0,4:4:6:66,6,0 1 735426 . G A 1164.39 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=21.77;MQ0=29;QD=15.74 GT:AD:DP:GQ:PL 1/1:0,11:11:15:158,15,0 1/1:0,22:22:30:316,30,0 1/1:0,23:23:36:373,36,0 1/1:0,18:18:33:343,33,0 1 735682 . G C 1529.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.619;DP=118;Dels=0.00;FS=3.471;HaplotypeScore=0.8922;MLEAC=4;MLEAF=0.500;MQ=37.22;MQ0=2;MQRankSum=1.299;QD=12.97;ReadPosRankSum=0.362 GT:AD:DP:GQ:PL 0/1:10,11:21:99:284,0,170 0/1:14,21:35:99:526,0,336 0/1:21,18:40:99:481,0,490 0/1:10,12:22:99:271,0,244 1 736522 . A T 1091.40 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=28.36;MQ0=16;QD=20.21 GT:AD:DP:GQ:PL 1/1:0,20:20:39:445,39,0 1/1:0,6:6:15:174,15,0 1/1:0,13:13:24:267,24,0 1/1:0,14:15:21:231,21,0 1 736523 . T C 1194.38 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=28.50;MQ0=16;QD=21.33 GT:AD:DP:GQ:PL 1/1:0,20:20:39:450,39,0 1/1:0,7:7:18:202,18,0 1/1:0,13:13:24:273,24,0 1/1:0,16:16:27:295,27,0 1 737740 . G A 507.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.702;DP=198;Dels=0.00;FS=0.000;HaplotypeScore=0.3325;MLEAC=4;MLEAF=0.500;MQ=22.67;MQ0=74;MQRankSum=-2.568;QD=2.57;ReadPosRankSum=0.443 GT:AD:DP:GQ:PL 0/1:38,9:47:46:46,0,506 0/1:37,13:50:99:218,0,558 0/1:30,15:45:76:76,0,484 0/1:41,15:56:99:200,0,537 1 739210 . A G 2682.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=0.771;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=0.2892;MLEAC=8;MLEAF=1.00;MQ=35.15;MQ0=16;MQRankSum=4.759;QD=23.12;ReadPosRankSum=1.014 GT:AD:DP:GQ:PL 1/1:6,24:30:54:625,54,0 1/1:6,21:27:51:561,51,0 1/1:3,33:36:84:931,84,0 1/1:2,21:23:54:591,54,0 1 739426 . A G 2224.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=1.686;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=1.7862;MLEAC=8;MLEAF=1.00;MQ=30.94;MQ0=25;MQRankSum=-1.732;QD=22.02;ReadPosRankSum=-0.069 GT:AD:DP:GQ:PL 1/1:0,21:22:45:520,45,0 1/1:0,27:27:60:652,60,0 1/1:0,27:27:51:574,51,0 1/1:1,23:25:45:504,45,0 1 739528 . G A 2236.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=87;Dels=0.00;FS=0.000;HaplotypeScore=1.6248;MLEAC=8;MLEAF=1.00;MQ=33.99;MQ0=11;QD=25.71 GT:AD:DP:GQ:PL 1/1:0,15:15:33:365,33,0 1/1:0,22:23:54:606,54,0 1/1:0,19:19:42:460,42,0 1/1:0,30:30:75:831,75,0 1 741579 . T C 1364.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=1.1951;MLEAC=8;MLEAF=1.00;MQ=22.64;MQ0=22;QD=17.05 GT:AD:DP:GQ:PL 1/1:0,21:22:39:398,39,0 1/1:0,17:17:24:224,24,0 1/1:0,15:15:36:366,36,0 1/1:0,25:26:42:402,42,0 1 743021 . T C 651.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.995;DP=146;Dels=0.00;FS=1.824;HaplotypeScore=0.7067;MLEAC=4;MLEAF=0.500;MQ=20.76;MQ0=64;MQRankSum=-3.163;QD=4.47;ReadPosRankSum=0.565 GT:AD:DP:GQ:PL 0/1:25,11:36:99:146,0,306 0/1:22,10:32:58:58,0,347 0/1:21,16:37:99:213,0,242 0/1:23,18:41:99:267,0,226 1 743072 . C A 3367.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=152;Dels=0.00;FS=0.000;HaplotypeScore=0.6606;MLEAC=8;MLEAF=1.00;MQ=27.04;MQ0=37;QD=22.15 GT:AD:DP:GQ:PL 1/1:8,28:36:63:672,63,0 1/1:5,37:42:99:1032,99,0 1/1:3,26:29:66:655,66,0 1/1:3,42:45:99:1034,102,0 1 744304 . C T 1453.12 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=2.262;DP=167;Dels=0.00;FS=48.875;HaplotypeScore=0.3898;MLEAC=5;MLEAF=0.625;MQ=16.69;MQ0=81;MQRankSum=0.945;QD=8.70;ReadPosRankSum=-0.201 GT:AD:DP:GQ:PL 0/1:11,27:38:56:411,0,56 1/1:18,23:41:15:384,15,0 0/1:18,16:34:92:273,0,92 0/1:27,27:54:99:419,0,147 1 745123 . A C 154.91 HARD_TO_VALIDATE AC=2;AF=0.250;AN=8;BaseQRankSum=-0.776;DP=174;Dels=0.00;FS=17.918;HaplotypeScore=2.2102;MLEAC=2;MLEAF=0.250;MQ=30.03;MQ0=58;MQRankSum=-0.107;QD=2.04;ReadPosRankSum=-0.633 GT:AD:DP:GQ:PL 0/0:57,3:60:96:0,96,1092 0/1:31,7:38:99:126,0,566 0/1:30,8:38:63:63,0,548 0/0:32,4:36:26:0,26,662 1 745347 . T C 284.10 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=-0.055;DP=159;Dels=0.00;FS=1.908;HaplotypeScore=1.6568;MLEAC=2;MLEAF=0.250;MQ=33.71;MQ0=6;MQRankSum=-0.919;QD=3.74;ReadPosRankSum=-4.901 GT:AD:DP:GQ:PL 0/0:43,3:47:73:0,73,1251 0/1:29,14:43:99:276,0,673 0/0:32,4:36:5:0,5,865 0/1:28,5:33:41:41,0,799 1 746368 . C A 64.12 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.598;DP=156;Dels=0.00;FS=4.107;HaplotypeScore=2.3610;MLEAC=3;MLEAF=0.375;MQ=33.22;MQ0=6;MQRankSum=-6.074;QD=0.59;ReadPosRankSum=1.218 GT:AD:DP:GQ:PL 0/1:24,7:32:63:63,0,621 0/0:39,8:47:9:0,9,1119 0/1:27,6:33:31:31,0,716 0/1:37,7:44:1:1,0,1021 1 748878 . G T 3183.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=149;Dels=0.00;FS=0.000;HaplotypeScore=0.4461;MLEAC=8;MLEAF=1.00;MQ=24.97;MQ0=30;QD=21.36 GT:AD:DP:GQ:PL 1/1:3,33:36:72:750,72,0 1/1:5,38:43:87:877,87,0 1/1:4,34:38:87:890,87,0 1/1:2,29:31:69:692,69,0 1 749265 . G A 564.68 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=11.37;MQ0=76;QD=5.88 GT:AD:DP:GQ:PL 1/1:11,8:19:6:59,6,0 1/1:15,14:29:15:150,15,0 1/1:9,17:26:18:174,18,0 1/1:10,12:22:21:207,21,0 1 749517 . C T 71.45 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=0.203;DP=93;Dels=0.00;FS=0.000;HaplotypeScore=0.1446;MLEAC=2;MLEAF=0.250;MQ=12.82;MQ0=62;MQRankSum=-0.880;QD=1.32;ReadPosRankSum=0.519 GT:AD:DP:GQ:PL 0/0:19,2:21:12:0,12,124 0/1:18,8:26:70:70,0,101 0/0:16,2:18:12:0,12,111 0/1:23,5:28:35:35,0,158 1 749592 . G A 152.18 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=9.81;MQ0=33;QD=3.46 GT:AD:DP:GQ:PL 1/1:0,13:13:6:61,6,0 1/1:0,8:8:3:32,3,0 1/1:0,9:9:6:57,6,0 1/1:0,14:14:3:26,3,0 1 749644 . T C 73.52 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.058;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.1663;MLEAC=4;MLEAF=0.500;MQ=12.19;MQ0=34;MQRankSum=-0.289;QD=1.93;ReadPosRankSum=0.521 GT:AD:DP:GQ:PL 0/1:10,5:15:21:52,0,21 1/1:5,3:8:3:32,3,0 0/0:4,7:11:3:0,3,32 0/1:9,6:15:21:21,0,46 1 749683 . C G 65 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=1.4989;MLEAC=4;MLEAF=1.00;MQ=12.08;MQ0=19;QD=3.42 GT:AD:DP:GQ:PL 1/1:1,9:10:3:30,3,0 ./. ./. 1/1:1,8:9:6:59,6,0 1 749720 . A G 56.09 HARD_TO_VALIDATE AC=4;AF=0.667;AN=6;BaseQRankSum=0.000;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.1928;MLEAC=5;MLEAF=0.833;MQ=16.04;MQ0=14;MQRankSum=-0.720;QD=4.01;ReadPosRankSum=0.720 GT:AD:DP:GQ:PL 1/1:6,4:10:6:53,6,0 1/1:2,2:4:3:32,3,0 0/0:3,1:4:3:0,3,26 ./. 1 749856 . C T 1166.92 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=4.360;DP=85;Dels=0.00;FS=8.614;HaplotypeScore=0.2290;MLEAC=7;MLEAF=0.875;MQ=24.04;MQ0=18;MQRankSum=2.233;QD=13.73;ReadPosRankSum=0.976 GT:AD:DP:GQ:PL 1/1:4,20:24:33:367,33,0 1/1:2,17:19:12:330,12,0 1/1:4,17:21:8:321,8,0 0/1:4,17:21:26:180,0,26 1 749989 . C T 480.08 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.2367;MLEAC=8;MLEAF=1.00;MQ=29.01;MQ0=7;QD=20.00 GT:AD:DP:GQ:PL 1/1:1,6:7:9:102,9,0 1/1:0,8:8:18:189,18,0 1/1:0,3:3:3:36,3,0 1/1:0,6:6:15:178,15,0 1 749997 . A G 357.27 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.2367;MLEAC=8;MLEAF=1.00;MQ=28.58;MQ0=7;QD=16.24 GT:AD:DP:GQ:PL 1/1:1,6:7:9:98,9,0 1/1:0,7:7:12:137,12,0 1/1:0,3:3:3:38,3,0 1/1:0,5:5:9:109,9,0 1 750013 . C T 63 HARD_TO_VALIDATE AC=4;AF=1.00;AN=4;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=16.63;MQ0=5;QD=12.60 GT:AD:DP:GQ:PL ./. 1/1:0,4:4:6:53,6,0 1/1:0,1:1:3:34,3,0 ./. 1 750342 . C T 54.80 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=10.80;MQ0=20;QD=3.04 GT:AD:DP:GQ:PL 1/1:1,6:8:3:24,3,0 ./. 1/1:0,6:6:3:24,3,0 1/1:0,4:4:3:30,3,0 1 752566 . G A 4818.35 PASS AC=8;AF=1.00;AN=8;DP=144;Dels=0.00;FS=0.000;HaplotypeScore=0.2290;MLEAC=8;MLEAF=1.00;MQ=57.23;MQ0=0;QD=33.46 GT:AD:DP:GQ:PL 1/1:0,34:34:99:1138,99,0 1/1:0,43:43:99:1453,129,0 1/1:0,32:32:93:1070,93,0 1/1:0,35:35:99:1183,105,0 1 752721 . A G 5412.35 PASS AC=8;AF=1.00;AN=8;DP=160;Dels=0.00;FS=0.000;HaplotypeScore=1.1213;MLEAC=8;MLEAF=1.00;MQ=59.94;MQ0=0;QD=33.83 GT:AD:DP:GQ:PL 1/1:0,42:42:99:1448,123,0 1/1:0,45:45:99:1531,135,0 1/1:0,32:32:93:1084,93,0 1/1:0,41:41:99:1375,120,0 1 752894 . T C 1966.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=140;Dels=0.00;FS=0.000;HaplotypeScore=0.8434;MLEAC=8;MLEAF=1.00;MQ=30.61;MQ0=54;QD=14.05 GT:AD:DP:GQ:PL 1/1:12,25:37:63:583,63,0 1/1:9,23:32:51:459,51,0 1/1:5,23:28:45:414,45,0 1/1:8,35:43:60:536,60,0 1 753269 . C G 1769.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=0.1663;MLEAC=8;MLEAF=1.00;MQ=28.65;MQ0=36;QD=18.82 GT:AD:DP:GQ:PL 1/1:0,14:14:24:266,24,0 1/1:0,19:19:30:341,30,0 1/1:0,28:28:45:508,45,0 1/1:0,33:33:60:680,60,0 1 753405 . C A 2157.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=2.2218;MLEAC=8;MLEAF=1.00;MQ=33.63;MQ0=14;QD=20.95 GT:AD:DP:GQ:PL 1/1:0,23:23:36:405,36,0 1/1:0,27:28:57:621,57,0 1/1:0,25:25:45:484,45,0 1/1:0,27:27:63:673,63,0 1 753425 . T C 1990.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=1.3760;MLEAC=8;MLEAF=1.00;MQ=31.17;MQ0=22;QD=19.71 GT:AD:DP:GQ:PL 1/1:0,20:20:27:317,27,0 1/1:0,27:27:51:580,51,0 1/1:0,28:28:42:471,42,0 1/1:0,26:26:60:648,60,0 1 753474 . C G 2167.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=0.6912;MLEAC=8;MLEAF=1.00;MQ=37.21;MQ0=9;QD=26.76 GT:AD:DP:GQ:PL 1/1:0,16:16:39:445,39,0 1/1:0,21:21:51:554,51,0 1/1:0,22:23:54:604,54,0 1/1:0,21:21:51:590,51,0 1 753849 . G T 644.50 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=18.77;MQ0=5;QD=14.32 GT:AD:DP:GQ:PL 1/1:0,13:13:24:217,24,0 1/1:0,9:9:12:109,12,0 1/1:0,11:11:12:103,12,0 1/1:0,12:12:27:241,27,0 1 754182 . A G 2932.35 PASS AC=8;AF=1.00;AN=8;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=0.2497;MLEAC=8;MLEAF=1.00;MQ=54.60;MQ0=0;QD=29.32 GT:AD:DP:GQ:PL 1/1:0,24:24:69:747,69,0 1/1:0,27:27:75:763,75,0 1/1:0,21:21:57:574,57,0 1/1:0,28:28:84:874,84,0 1 754192 . A G 2909.35 PASS AC=8;AF=1.00;AN=8;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=0.2497;MLEAC=8;MLEAF=1.00;MQ=53.94;MQ0=0;QD=29.69 GT:AD:DP:GQ:PL 1/1:0,21:21:63:662,63,0 1/1:0,26:26:75:763,75,0 1/1:0,23:23:63:631,63,0 1/1:0,28:28:81:879,81,0 1 754334 . T C 4581.35 PASS AC=8;AF=1.00;AN=8;DP=156;Dels=0.00;FS=0.000;HaplotypeScore=2.1762;MLEAC=8;MLEAF=1.00;MQ=52.11;MQ0=0;QD=29.37 GT:AD:DP:GQ:PL 1/1:0,35:36:99:1034,99,0 1/1:0,46:46:99:1325,129,0 1/1:0,34:34:99:1058,102,0 1/1:0,40:40:99:1190,120,0 1 754503 . G A 4580.35 PASS AC=8;AF=1.00;AN=8;DP=138;Dels=0.00;FS=0.000;HaplotypeScore=0.1835;MLEAC=8;MLEAF=1.00;MQ=58.95;MQ0=0;QD=33.19 GT:AD:DP:GQ:PL 1/1:0,31:31:90:1049,90,0 1/1:0,35:35:99:1159,102,0 1/1:0,35:35:99:1213,105,0 1/1:0,36:37:99:1185,105,0 1 754964 . C T 4652.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=-1.054;DP=143;Dels=0.00;FS=0.000;HaplotypeScore=1.8187;MLEAC=8;MLEAF=1.00;MQ=41.23;MQ0=0;MQRankSum=1.490;QD=32.53;ReadPosRankSum=-0.884 GT:AD:DP:GQ:PL 1/1:1,44:45:95:1373,95,0 1/1:0,32:32:96:1073,96,0 1/1:0,25:25:75:833,75,0 1/1:0,41:41:99:1399,123,0 1 755775 . A G 3165.34 PASS AC=7;AF=0.875;AN=8;BaseQRankSum=-0.487;DP=174;Dels=0.00;FS=1.116;HaplotypeScore=4.8562;MLEAC=7;MLEAF=0.875;MQ=59.23;MQ0=0;MQRankSum=2.104;QD=18.19;ReadPosRankSum=0.897 GT:AD:DP:GQ:PL 0/1:5,24:33:36:529,0,36 1/1:4,54:58:99:1148,99,0 1/1:2,43:45:36:843,36,0 1/1:2,34:38:46:677,46,0 1 755887 . C G 5711.35 PASS AC=8;AF=1.00;AN=8;DP=178;Dels=0.00;FS=0.000;HaplotypeScore=3.2938;MLEAC=8;MLEAF=1.00;MQ=52.19;MQ0=0;QD=32.09 GT:AD:DP:GQ:PL 1/1:0,60:60:99:1908,165,0 1/1:0,33:33:96:1085,96,0 1/1:0,43:44:99:1370,120,0 1/1:0,41:41:99:1374,123,0 1 755890 . A T 5678.35 PASS AC=8;AF=1.00;AN=8;DP=173;Dels=0.00;FS=0.000;HaplotypeScore=5.5446;MLEAC=8;MLEAF=1.00;MQ=52.05;MQ0=0;QD=32.82 GT:AD:DP:GQ:PL 1/1:0,57:57:99:1856,159,0 1/1:0,32:32:90:1044,90,0 1/1:0,44:44:99:1426,126,0 1/1:0,40:40:99:1378,120,0 1 755940 . C T 4126.38 PASS AC=5;AF=0.625;AN=8;BaseQRankSum=3.369;DP=232;Dels=0.00;FS=0.000;HaplotypeScore=25.1682;MLEAC=5;MLEAF=0.625;MQ=48.33;MQ0=5;MQRankSum=8.523;QD=17.79;ReadPosRankSum=-3.312 GT:AD:DP:GQ:PL 0/1:15,39:55:4:1034,0,4 0/1:19,38:57:51:1009,0,51 0/1:23,35:58:99:895,0,229 1/1:14,48:62:25:1221,25,0 1 756011 . A C 44.33 LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-2.421;DP=209;Dels=0.00;FS=26.240;HaplotypeScore=3.4770;MLEAC=1;MLEAF=0.125;MQ=56.98;MQ0=1;MQRankSum=-1.601;QD=0.66;ReadPosRankSum=-3.306 GT:AD:DP:GQ:PL 0/0:49,4:54:78:0,78,1442 0/1:47,19:67:76:76,0,1136 0/0:41,6:47:72:0,72,1238 0/0:34,6:41:44:0,44,972 1 756040 . G A 50.58 LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=0.566;DP=243;Dels=0.00;FS=49.551;HaplotypeScore=6.5087;MLEAC=1;MLEAF=0.125;MQ=55.20;MQ0=1;MQRankSum=-8.273;QD=0.78;ReadPosRankSum=-1.272 GT:AD:DP:GQ:PL 0/1:55,9:65:82:82,0,1321 0/0:63,8:72:10:0,10,1615 0/0:50,9:59:29:0,29,1411 0/0:43,4:47:29:0,29,1166 1 756042 . G C 145.04 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-0.674;DP=241;Dels=0.00;FS=21.696;HaplotypeScore=6.1258;MLEAC=3;MLEAF=0.375;MQ=55.15;MQ0=1;MQRankSum=-7.535;QD=0.79;ReadPosRankSum=-1.510 GT:AD:DP:GQ:PL 0/1:51,14:65:99:128,0,1154 0/1:58,13:71:14:14,0,1345 0/0:45,13:58:8:0,8,1217 0/1:38,9:47:36:36,0,917 1 756063 . A C 338.94 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.270;DP=260;Dels=0.00;FS=4.121;HaplotypeScore=16.9840;MLEAC=4;MLEAF=0.500;MQ=54.20;MQ0=4;MQRankSum=-6.688;QD=1.30;ReadPosRankSum=2.906 GT:AD:DP:GQ:PL 0/1:54,21:75:99:109,0,1405 0/1:49,22:72:99:127,0,1291 0/1:41,16:57:39:39,0,1183 0/1:37,19:56:96:96,0,922 1 756250 . G A 117.52 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.590;DP=219;Dels=0.00;FS=0.000;HaplotypeScore=8.4198;MLEAC=3;MLEAF=0.375;MQ=52.95;MQ0=2;MQRankSum=-6.950;QD=0.71;ReadPosRankSum=-4.042 GT:AD:DP:GQ:PL 0/1:49,7:56:34:34,0,1235 0/1:61,7:68:1:1,0,1641 0/1:34,8:42:99:114,0,818 0/0:46,7:53:19:0,19,1175 1 756257 . A C 253.08 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-1.318;DP=216;Dels=0.00;FS=0.000;HaplotypeScore=10.5557;MLEAC=3;MLEAF=0.375;MQ=51.83;MQ0=2;MQRankSum=-6.174;QD=1.58;ReadPosRankSum=-1.020 GT:AD:DP:GQ:PL 0/1:40,16:56:99:128,0,990 0/1:53,9:62:37:37,0,1314 0/1:32,9:42:99:122,0,767 0/0:46,9:56:16:0,16,1212 1 756259 . G A 255.93 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-0.432;DP=217;Dels=0.00;FS=1.445;HaplotypeScore=13.6878;MLEAC=4;MLEAF=0.500;MQ=51.51;MQ0=2;MQRankSum=-4.892;QD=1.58;ReadPosRankSum=-2.826 GT:AD:DP:GQ:PL 0/1:47,8:55:62:62,0,1262 0/1:53,10:63:64:64,0,1344 0/1:34,10:44:99:161,0,857 0/0:47,8:55:2:0,2,1108 1 756267 . T G 45.64 LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-7.485;DP=314;Dels=0.00;FS=8.064;HaplotypeScore=33.8445;MLEAC=2;MLEAF=0.250;MQ=51.30;MQ0=5;MQRankSum=-6.915;QD=0.32;ReadPosRankSum=0.812 GT:AD:DP:GQ:PL 0/0:75,10:85:21:0,21,2011 0/0:77,8:85:80:0,80,2133 0/1:56,8:64:10:10,0,1351 0/1:69,11:80:69:69,0,1610 1 756268 . G A 4618.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.444;DP=313;Dels=0.00;FS=28.118;HaplotypeScore=31.3386;MLEAC=4;MLEAF=0.500;MQ=51.09;MQ0=5;MQRankSum=-2.270;QD=14.76;ReadPosRankSum=9.250 GT:AD:DP:GQ:PL 0/1:30,55:85:99:1329,0,591 0/1:29,52:86:99:1285,0,489 0/1:24,39:65:99:815,0,457 0/1:20,52:77:99:1222,0,333 1 756277 . G T 2219.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.021;DP=415;Dels=0.00;FS=0.000;HaplotypeScore=45.0358;MLEAC=4;MLEAF=0.500;MQ=47.66;MQ0=11;MQRankSum=-10.049;QD=5.35;ReadPosRankSum=-6.449 GT:AD:DP:GQ:PL 0/1:88,33:122:99:661,0,2086 0/1:78,30:109:99:483,0,1963 0/1:51,26:78:99:448,0,1242 0/1:63,38:105:99:660,0,1422 1 756334 . C T 3001.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.927;DP=339;Dels=0.00;FS=12.334;HaplotypeScore=5.7595;MLEAC=4;MLEAF=0.500;MQ=48.41;MQ0=2;MQRankSum=-11.613;QD=8.86;ReadPosRankSum=4.964 GT:AD:DP:GQ:PL 0/1:66,36:104:99:758,0,1645 0/1:50,41:91:99:955,0,1201 0/1:36,25:61:99:575,0,995 0/1:49,34:83:99:746,0,1272 1 756347 . C G 252.94 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-3.502;DP=245;Dels=0.00;FS=0.000;HaplotypeScore=5.5267;MLEAC=4;MLEAF=0.500;MQ=51.74;MQ0=0;MQRankSum=-8.261;QD=1.03;ReadPosRankSum=4.227 GT:AD:DP:GQ:PL 0/1:69,13:82:38:38,0,2003 0/1:47,15:62:99:127,0,1206 0/1:39,8:47:46:46,0,1175 0/1:45,9:54:74:74,0,1226 1 756348 . A C 387.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.827;DP=240;Dels=0.00;FS=0.000;HaplotypeScore=5.2775;MLEAC=4;MLEAF=0.500;MQ=51.83;MQ0=0;MQRankSum=-7.758;QD=1.62;ReadPosRankSum=3.911 GT:AD:DP:GQ:PL 0/1:67,14:81:99:132,0,1671 0/1:46,13:59:99:136,0,1196 0/1:39,7:46:63:63,0,1150 0/1:43,11:54:89:89,0,1122 1 756349 . A C 413.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.678;DP=238;Dels=0.00;FS=1.291;HaplotypeScore=5.4477;MLEAC=4;MLEAF=0.500;MQ=51.89;MQ0=0;MQRankSum=-8.014;QD=1.74;ReadPosRankSum=4.203 GT:AD:DP:GQ:PL 0/1:67,14:81:99:135,0,1696 0/1:44,13:57:99:144,0,1108 0/1:37,9:46:80:80,0,1066 0/1:45,9:54:87:87,0,1134 1 756352 . C T 153.12 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-4.116;DP=245;Dels=0.00;FS=2.716;HaplotypeScore=6.0658;MLEAC=3;MLEAF=0.375;MQ=50.71;MQ0=0;MQRankSum=-6.976;QD=0.83;ReadPosRankSum=3.559 GT:AD:DP:GQ:PL 0/1:71,11:82:13:13,0,2123 0/1:45,12:57:99:103,0,1238 0/1:39,7:46:71:71,0,1127 0/0:54,6:60:38:0,38,1540 1 756361 . C A 147.45 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.440;DP=254;Dels=0.00;FS=0.000;HaplotypeScore=3.9341;MLEAC=4;MLEAF=0.500;MQ=50.63;MQ0=1;MQRankSum=-7.325;QD=0.75;ReadPosRankSum=0.663 GT:AD:DP:GQ:PL 0/1:76,12:88:9:9,0,2181 0/1:50,13:63:99:99,0,1334 0/1:39,7:46:69:69,0,1128 0/0:49,7:56:0:0,0,1411 1 756364 . G A 159.91 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.041;DP=254;Dels=0.00;FS=0.000;HaplotypeScore=4.6359;MLEAC=3;MLEAF=0.375;MQ=50.72;MQ0=1;MQRankSum=-7.493;QD=0.81;ReadPosRankSum=-0.375 GT:AD:DP:GQ:PL 0/1:76,13:89:33:33,0,2255 0/1:50,13:63:97:97,0,1268 0/1:39,7:46:64:64,0,1159 0/0:49,6:56:35:0,35,1496 1 756373 . A G 67.95 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.392;DP=249;Dels=0.00;FS=0.000;HaplotypeScore=15.2694;MLEAC=3;MLEAF=0.375;MQ=50.42;MQ0=1;MQRankSum=-7.102;QD=0.34;ReadPosRankSum=-3.513 GT:AD:DP:GQ:PL 0/1:64,11:78:28:28,0,1893 0/1:57,12:70:64:64,0,1371 0/1:44,6:50:8:8,0,1144 0/0:44,5:51:6:0,6,1175 1 756378 . G C 296.95 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.929;DP=245;Dels=0.00;FS=0.000;HaplotypeScore=18.4817;MLEAC=4;MLEAF=0.500;MQ=50.49;MQ0=1;MQRankSum=-8.765;QD=1.21;ReadPosRankSum=-4.465 GT:AD:DP:GQ:PL 0/1:60,12:72:31:31,0,1632 0/1:50,20:70:99:174,0,1174 0/1:40,10:50:74:74,0,1100 0/1:41,12:53:50:50,0,824 1 756380 . T A 5312.95 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.796;DP=244;Dels=0.00;FS=1.268;HaplotypeScore=23.1633;MLEAC=4;MLEAF=0.500;MQ=50.49;MQ0=1;MQRankSum=9.413;QD=21.77;ReadPosRankSum=4.182 GT:AD:DP:GQ:PL 0/1:12,59:71:39:1758,0,39 0/1:20,51:72:99:1309,0,149 0/1:9,41:50:74:1189,0,74 0/1:7,43:50:29:1089,0,29 1 756430 . A C 51.90 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-3.951;DP=234;Dels=0.00;FS=33.754;HaplotypeScore=12.0221;MLEAC=2;MLEAF=0.250;MQ=53.54;MQ0=1;MQRankSum=-5.236;QD=0.44;ReadPosRankSum=0.264 GT:AD:DP:GQ:PL 0/0:56,10:66:77:0,77,1703 0/1:47,16:63:40:40,0,1152 0/0:41,8:49:48:0,48,1121 0/1:43,12:56:46:46,0,1083 1 756604 . A G 5476.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=2.034;DP=210;Dels=0.00;FS=0.000;HaplotypeScore=3.4679;MLEAC=8;MLEAF=1.00;MQ=59.29;MQ0=0;MQRankSum=1.785;QD=26.08;ReadPosRankSum=1.192 GT:AD:DP:GQ:PL 1/1:2,75:79:99:2052,183,0 1/1:0,44:44:99:1222,120,0 1/1:0,39:39:99:1078,105,0 1/1:0,47:48:99:1150,114,0 1 757640 . G A 6146.35 PASS AC=8;AF=1.00;AN=8;DP=198;Dels=0.00;FS=0.000;HaplotypeScore=3.7112;MLEAC=8;MLEAF=1.00;MQ=59.88;MQ0=0;QD=31.04 GT:AD:DP:GQ:PL 1/1:0,54:59:99:1698,150,0 1/1:0,54:55:99:1713,156,0 1/1:0,35:35:99:1158,102,0 1/1:0,49:49:99:1603,144,0 1 757734 . C T 5932.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=2.141;DP=194;Dels=0.00;FS=6.239;HaplotypeScore=3.0101;MLEAC=8;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.331;QD=30.58;ReadPosRankSum=-0.019 GT:AD:DP:GQ:PL 1/1:5,55:60:99:1665,111,0 1/1:0,52:52:99:1667,150,0 1/1:0,42:42:99:1354,123,0 1/1:0,40:40:99:1272,114,0 1 757842 . G C 940.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-3.564;DP=132;Dels=0.00;FS=14.006;HaplotypeScore=8.1450;MLEAC=4;MLEAF=0.500;MQ=53.41;MQ0=3;MQRankSum=0.038;QD=7.13;ReadPosRankSum=-1.846 GT:AD:DP:GQ:PL 0/1:18,13:32:99:235,0,472 0/1:24,12:36:99:206,0,645 0/1:18,13:31:99:265,0,535 0/1:18,15:33:99:267,0,371 1 757843 . C A 1361.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.856;DP=133;Dels=0.00;FS=13.310;HaplotypeScore=8.3939;MLEAC=4;MLEAF=0.500;MQ=53.35;MQ0=3;MQRankSum=0.352;QD=10.24;ReadPosRankSum=1.134 GT:AD:DP:GQ:PL 0/1:19,13:32:99:305,0,358 0/1:17,20:37:99:416,0,256 0/1:17,15:32:99:403,0,352 0/1:19,13:32:99:270,0,399 1 757869 . T C 199.01 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=2.735;DP=138;Dels=0.00;FS=0.000;HaplotypeScore=5.5208;MLEAC=4;MLEAF=0.500;MQ=54.23;MQ0=3;MQRankSum=-4.241;QD=1.44;ReadPosRankSum=-4.684 GT:AD:DP:GQ:PL 0/1:33,4:37:54:54,0,815 0/1:30,7:37:81:81,0,763 0/1:27,6:33:80:80,0,649 0/1:25,6:31:16:16,0,525 1 757936 . C A 5912.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=2.451;DP=201;Dels=0.00;FS=0.000;HaplotypeScore=4.6945;MLEAC=8;MLEAF=1.00;MQ=59.88;MQ0=0;MQRankSum=0.166;QD=29.41;ReadPosRankSum=0.711 GT:AD:DP:GQ:PL 1/1:3,56:59:99:1591,113,0 1/1:1,51:52:99:1554,141,0 1/1:0,41:42:99:1280,114,0 1/1:1,46:47:99:1513,135,0 1 758093 . T C 66.33 LowQD AC=1;AF=0.125;AN=8;BaseQRankSum=-6.274;DP=234;Dels=0.00;FS=1.210;HaplotypeScore=3.0517;MLEAC=1;MLEAF=0.125;MQ=59.25;MQ0=0;MQRankSum=-2.696;QD=0.98;ReadPosRankSum=-2.008 GT:AD:DP:GQ:PL 0/1:49,19:68:98:98,0,1399 0/0:61,7:68:99:0,126,1552 0/0:47,2:49:99:0,129,1454 0/0:44,5:49:93:0,93,1212 1 758144 . A G 6668.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=0.805;DP=209;Dels=0.00;FS=0.000;HaplotypeScore=4.5709;MLEAC=8;MLEAF=1.00;MQ=59.01;MQ0=0;MQRankSum=3.814;QD=31.91;ReadPosRankSum=-0.296 GT:AD:DP:GQ:PL 1/1:4,56:60:99:1801,112,0 1/1:1,61:62:99:1959,177,0 1/1:0,45:45:99:1503,135,0 1/1:0,42:42:99:1431,126,0 1 758324 . T C 6445.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.698;DP=201;Dels=0.00;FS=0.000;HaplotypeScore=2.2503;MLEAC=8;MLEAF=1.00;MQ=59.38;MQ0=0;MQRankSum=1.370;QD=32.07;ReadPosRankSum=0.698 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2029,180,0 1/1:0,47:47:99:1494,138,0 1/1:0,43:43:99:1406,126,0 1/1:1,48:49:99:1542,141,0 1 758626 . C T 6270.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=2.324;DP=200;Dels=0.00;FS=0.000;HaplotypeScore=7.9293;MLEAC=8;MLEAF=1.00;MQ=58.49;MQ0=1;MQRankSum=1.735;QD=31.35;ReadPosRankSum=-1.660 GT:AD:DP:GQ:PL 1/1:0,63:64:99:2009,177,0 1/1:0,54:54:99:1717,153,0 1/1:2,38:40:99:1277,114,0 1/1:1,41:42:99:1293,114,0 1 759700 . T C 883.42 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=26.16;MQ0=12;QD=18.80 GT:AD:DP:GQ:PL 1/1:0,12:12:30:335,30,0 1/1:0,13:13:15:149,15,0 1/1:0,10:10:18:195,18,0 1/1:0,12:12:21:230,21,0 1 759837 . T A 2367.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=1.4446;MLEAC=8;MLEAF=1.00;MQ=40.36;MQ0=11;QD=26.90 GT:AD:DP:GQ:PL 1/1:0,16:16:39:428,39,0 1/1:0,30:30:72:779,72,0 1/1:0,19:19:51:578,51,0 1/1:0,23:23:57:608,57,0 1 760912 . C T 5179.35 PASS AC=8;AF=1.00;AN=8;DP=157;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=51.44;MQ0=0;QD=32.99 GT:AD:DP:GQ:PL 1/1:0,33:33:87:1003,87,0 1/1:0,36:36:99:1210,105,0 1/1:0,46:46:99:1587,138,0 1/1:0,42:42:99:1405,123,0 1 761147 . T C 5791.35 PASS AC=8;AF=1.00;AN=8;DP=169;Dels=0.00;FS=0.000;HaplotypeScore=0.8662;MLEAC=8;MLEAF=1.00;MQ=57.58;MQ0=0;QD=34.27 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1149,99,0 1/1:0,47:47:99:1620,141,0 1/1:0,42:42:99:1427,126,0 1/1:0,47:47:99:1621,141,0 1 761732 . C T 1995.35 PASS AC=8;AF=1.00;AN=8;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.5973;MLEAC=8;MLEAF=1.00;MQ=40.71;MQ0=3;QD=28.51 GT:AD:DP:GQ:PL 1/1:0,18:18:39:431,39,0 1/1:0,15:15:42:462,42,0 1/1:0,14:14:42:481,42,0 1/1:0,23:23:57:647,57,0 1 761752 . C T 1261.36 PASS AC=8;AF=1.00;AN=8;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=34.90;MQ0=5;QD=25.23 GT:AD:DP:GQ:PL 1/1:0,16:16:27:291,27,0 1/1:0,11:11:30:323,30,0 1/1:0,10:10:30:333,30,0 1/1:0,13:13:30:340,30,0 1 761800 . A T 630.55 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=21.77;MQ0=7;QD=19.11 GT:AD:DP:GQ:PL 1/1:0,8:8:15:158,15,0 1/1:0,9:9:21:221,21,0 1/1:0,5:5:9:89,9,0 1/1:0,11:11:18:188,18,0 1 761811 . G A 954.46 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7481;MLEAC=8;MLEAF=1.00;MQ=27.06;MQ0=7;QD=22.20 GT:AD:DP:GQ:PL 1/1:0,8:8:15:158,15,0 1/1:0,13:13:33:367,33,0 1/1:0,6:6:12:134,12,0 1/1:0,16:16:30:321,30,0 1 762273 . G A 1972.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=31.44;MQ0=8;QD=26.30 GT:AD:DP:GQ:PL 1/1:0,25:25:69:774,69,0 1/1:0,15:15:36:385,36,0 1/1:0,18:18:42:457,42,0 1/1:0,17:17:36:382,36,0 1 762589 . G C 2601.35 PASS AC=8;AF=1.00;AN=8;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=0.4972;MLEAC=8;MLEAF=1.00;MQ=38.85;MQ0=2;QD=26.01 GT:AD:DP:GQ:PL 1/1:0,26:27:66:688,66,0 1/1:0,31:31:81:815,81,0 1/1:1,20:21:48:510,48,0 1/1:0,21:21:60:614,60,0 1 762592 . C G 2596.35 PASS AC=8;AF=1.00;AN=8;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=0.8585;MLEAC=8;MLEAF=1.00;MQ=38.33;MQ0=4;QD=25.71 GT:AD:DP:GQ:PL 1/1:0,27:27:72:728,72,0 1/1:1,31:32:87:857,87,0 1/1:2,20:22:48:472,48,0 1/1:0,20:20:57:565,57,0 1 762601 . T C 3087.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.698;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=1.5417;MLEAC=8;MLEAF=1.00;MQ=38.19;MQ0=4;MQRankSum=0.978;QD=29.13;ReadPosRankSum=-0.257 GT:AD:DP:GQ:PL 1/1:1,27:28:81:877,81,0 1/1:1,32:33:87:941,87,0 1/1:2,20:22:51:565,51,0 1/1:0,23:23:66:730,66,0 1 762632 . T A 3420.35 PASS AC=8;AF=1.00;AN=8;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=1.1522;MLEAC=8;MLEAF=1.00;MQ=37.88;MQ0=4;QD=30.81 GT:AD:DP:GQ:PL 1/1:0,29:29:84:920,84,0 1/1:1,34:35:96:1068,96,0 1/1:2,18:20:51:583,51,0 1/1:0,26:26:78:875,78,0 1 763394 . G A 903.09 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.420;DP=83;Dels=0.00;FS=10.360;HaplotypeScore=0.2892;MLEAC=4;MLEAF=0.500;MQ=21.72;MQ0=33;MQRankSum=0.261;QD=10.88;ReadPosRankSum=0.352 GT:AD:DP:GQ:PL 0/1:13,6:19:35:35,0,154 0/1:8,17:25:41:356,0,41 0/1:8,15:23:0:253,0,0 0/1:3,13:16:20:289,0,20 1 766105 . T A 2488.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=137;Dels=0.00;FS=0.000;HaplotypeScore=0.5567;MLEAC=8;MLEAF=1.00;MQ=28.77;MQ0=59;QD=18.16 GT:AD:DP:GQ:PL 1/1:4,34:38:84:959,84,0 1/1:7,24:31:51:563,51,0 1/1:9,25:34:45:517,45,0 1/1:13,21:34:42:475,42,0 1 767780 . G A 4340.35 PASS AC=8;AF=1.00;AN=8;DP=138;Dels=0.00;FS=0.000;HaplotypeScore=0.9388;MLEAC=8;MLEAF=1.00;MQ=40.13;MQ0=1;QD=31.45 GT:AD:DP:GQ:PL 1/1:0,34:34:87:974,87,0 1/1:0,38:38:99:1170,108,0 1/1:0,38:38:99:1303,114,0 1/1:0,28:28:84:919,84,0 1 768253 . A C 3854.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=-0.028;DP=130;Dels=0.00;FS=3.160;HaplotypeScore=0.4623;MLEAC=8;MLEAF=1.00;MQ=46.85;MQ0=6;MQRankSum=0.251;QD=29.65;ReadPosRankSum=0.810 GT:AD:DP:GQ:PL 1/1:1,29:30:47:865,47,0 1/1:0,36:36:96:1078,96,0 1/1:3,26:29:75:827,75,0 1/1:0,35:35:99:1110,102,0 1 769829 . C A 3935.35 PASS AC=8;AF=1.00;AN=8;DP=127;Dels=0.00;FS=0.000;HaplotypeScore=0.6301;MLEAC=8;MLEAF=1.00;MQ=44.23;MQ0=3;QD=30.99 GT:AD:DP:GQ:PL 1/1:0,33:33:84:943,84,0 1/1:0,28:28:81:882,81,0 1/1:0,35:35:99:1199,105,0 1/1:0,30:31:84:937,84,0 1 770075 . C T 2648.35 PASS AC=8;AF=1.00;AN=8;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=34.25;MQ0=9;QD=27.30 GT:AD:DP:GQ:PL 1/1:0,29:29:69:782,69,0 1/1:0,24:24:60:644,60,0 1/1:0,26:26:72:785,72,0 1/1:0,18:18:42:463,42,0 1 770568 . A G 1024.37 PASS AC=8;AF=1.00;AN=8;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.0430;MLEAC=8;MLEAF=1.00;MQ=34.61;MQ0=4;QD=24.39 GT:AD:DP:GQ:PL 1/1:0,13:13:24:245,24,0 1/1:0,8:8:21:223,21,0 1/1:0,12:12:30:329,30,0 1/1:0,9:9:24:253,24,0 1 770918 . T G 822.39 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=23.73;MQ0=13;QD=18.69 GT:AD:DP:GQ:PL 1/1:0,11:11:18:174,18,0 1/1:0,13:13:24:237,24,0 1/1:0,8:8:21:235,21,0 1/1:0,12:12:21:202,21,0 1 771410 . C T 2794.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=-0.375;DP=169;Dels=0.00;FS=0.000;HaplotypeScore=0.9894;MLEAC=8;MLEAF=1.00;MQ=25.78;MQ0=71;MQRankSum=0.661;QD=16.53;ReadPosRankSum=0.339 GT:AD:DP:GQ:PL 1/1:12,29:41:54:580,54,0 1/1:5,34:39:87:930,87,0 1/1:11,32:43:41:732,41,0 1/1:14,31:46:54:578,54,0 1 771823 . T C 3212.34 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=145;Dels=0.00;FS=0.000;HaplotypeScore=1.1246;MLEAC=8;MLEAF=1.00;MQ=34.48;MQ0=17;QD=22.15 GT:AD:DP:GQ:PL 1/1:0,34:34:69:772,69,0 1/1:0,45:45:87:938,87,0 1/1:0,32:32:72:757,72,0 1/1:0,34:34:72:771,72,0 1 772755 . A C 2977.35 PASS AC=8;AF=1.00;AN=8;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.1835;MLEAC=8;MLEAF=1.00;MQ=54.39;MQ0=0;QD=30.69 GT:AD:DP:GQ:PL 1/1:0,23:23:69:722,69,0 1/1:0,24:24:72:723,72,0 1/1:0,23:23:69:746,69,0 1/1:0,27:27:75:812,75,0 1 774736 . A C 4662.35 PASS AC=8;AF=1.00;AN=8;DP=159;Dels=0.00;FS=0.000;HaplotypeScore=2.9516;MLEAC=8;MLEAF=1.00;MQ=47.68;MQ0=2;QD=29.32 GT:AD:DP:GQ:PL 1/1:0,40:40:99:1319,120,0 1/1:0,44:44:99:1252,114,0 1/1:0,38:38:99:1084,99,0 1/1:0,37:37:93:1033,93,0 1 774785 . G A 3679.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=-1.603;DP=137;Dels=0.00;FS=3.278;HaplotypeScore=6.6404;MLEAC=8;MLEAF=1.00;MQ=40.88;MQ0=2;MQRankSum=0.646;QD=26.86;ReadPosRankSum=0.259 GT:AD:DP:GQ:PL 1/1:0,28:28:78:840,78,0 1/1:0,40:40:99:1151,102,0 1/1:1,40:41:62:1029,62,0 1/1:0,27:27:63:685,63,0 1 774874 . A C 1572.57 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.620;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=3.2304;MLEAC=8;MLEAF=1.00;MQ=31.30;MQ0=2;MQRankSum=1.874;QD=23.47;ReadPosRankSum=1.715 GT:AD:DP:GQ:PL 1/1:1,15:16:42:463,42,0 1/1:1,22:23:54:558,54,0 1/1:1,12:14:7:264,7,0 1/1:0,14:14:30:313,30,0 1 774883 . G A 1185.18 PASS AC=6;AF=0.750;AN=8;BaseQRankSum=1.498;DP=69;Dels=0.00;FS=1.126;HaplotypeScore=3.0137;MLEAC=6;MLEAF=0.750;MQ=34.67;MQ0=2;MQRankSum=-1.153;QD=17.18;ReadPosRankSum=3.223 GT:AD:DP:GQ:PL 1/1:2,13:16:5:362,5,0 1/1:2,17:19:18:405,18,0 0/1:5,10:15:83:225,0,83 0/1:5,14:19:35:226,0,35 1 774900 . C G 426.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.944;DP=68;Dels=0.00;FS=2.097;HaplotypeScore=3.3988;MLEAC=4;MLEAF=0.500;MQ=35.27;MQ0=1;MQRankSum=-2.122;QD=6.28;ReadPosRankSum=-1.239 GT:AD:DP:GQ:PL 0/1:14,5:19:71:71,0,113 0/1:5,10:16:89:210,0,89 0/1:9,6:15:99:128,0,200 0/1:12,6:18:50:50,0,255 1 774923 . G C 1814.35 PASS AC=8;AF=1.00;AN=8;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=1.1275;MLEAC=8;MLEAF=1.00;MQ=40.68;MQ0=1;QD=26.68 GT:AD:DP:GQ:PL 1/1:0,16:16:45:472,45,0 1/1:0,17:17:45:458,45,0 1/1:0,14:14:39:394,39,0 1/1:0,21:21:48:516,48,0 1 774942 . G C 40.94 LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-2.949;DP=107;Dels=0.00;FS=15.456;HaplotypeScore=5.1172;MLEAC=2;MLEAF=0.250;MQ=44.89;MQ0=1;MQRankSum=-3.177;QD=0.74;ReadPosRankSum=0.059 GT:AD:DP:GQ:PL 0/1:18,8:27:46:46,0,354 0/0:21,5:26:0:0,0,398 0/0:23,3:26:26:0,26,478 0/1:21,7:28:26:26,0,431 1 774953 . G A 30.34 LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=-3.381;DP=130;Dels=0.00;FS=19.675;HaplotypeScore=4.4426;MLEAC=1;MLEAF=0.125;MQ=47.25;MQ0=1;MQRankSum=3.652;QD=0.87;ReadPosRankSum=-2.798 GT:AD:DP:GQ:PL 0/1:27,7:35:62:62,0,541 0/0:24,5:29:54:0,54,548 0/0:29,1:30:81:0,81,841 0/0:35,1:36:48:0,48,736 1 775426 . G A 3461.35 PASS AC=8;AF=1.00;AN=8;DP=113;Dels=0.00;FS=0.000;HaplotypeScore=0.3526;MLEAC=8;MLEAF=1.00;MQ=38.48;MQ0=0;QD=30.63 GT:AD:DP:GQ:PL 1/1:0,30:30:81:883,81,0 1/1:0,25:25:69:754,69,0 1/1:0,36:36:99:1130,102,0 1/1:0,22:22:66:720,66,0 1 775659 . A G 3132.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.697;DP=110;Dels=0.00;FS=0.000;HaplotypeScore=0.4251;MLEAC=8;MLEAF=1.00;MQ=44.46;MQ0=10;MQRankSum=-0.554;QD=28.48;ReadPosRankSum=-0.069 GT:AD:DP:GQ:PL 1/1:0,26:26:72:800,72,0 1/1:1,30:31:75:823,75,0 1/1:0,25:25:66:746,66,0 1/1:0,28:28:72:789,72,0 1 777122 . A T 4157.35 PASS AC=8;AF=1.00;AN=8;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=0.2080;MLEAC=8;MLEAF=1.00;MQ=54.10;MQ0=0;QD=33.26 GT:AD:DP:GQ:PL 1/1:0,32:32:90:1041,90,0 1/1:0,31:31:93:1056,93,0 1/1:0,28:28:84:965,84,0 1/1:0,33:34:99:1121,99,0 1 778569 . A G 4524.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.711;DP=166;Dels=0.00;FS=0.000;HaplotypeScore=2.2756;MLEAC=8;MLEAF=1.00;MQ=43.12;MQ0=3;MQRankSum=-0.414;QD=27.26;ReadPosRankSum=0.096 GT:AD:DP:GQ:PL 1/1:0,50:50:99:1276,120,0 1/1:0,39:39:99:1122,108,0 1/1:0,49:49:99:1468,132,0 1/1:1,27:28:66:684,66,0 1 780027 . G T 5389.35 PASS AC=8;AF=1.00;AN=8;DP=160;Dels=0.00;FS=0.000;HaplotypeScore=2.0997;MLEAC=8;MLEAF=1.00;MQ=59.04;MQ0=0;QD=33.68 GT:AD:DP:GQ:PL 1/1:0,32:32:90:1054,90,0 1/1:0,47:47:99:1603,138,0 1/1:0,37:37:99:1307,111,0 1/1:0,43:43:99:1451,126,0 1 780785 . T A 4637.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.660;DP=145;Dels=0.00;FS=0.000;HaplotypeScore=1.8405;MLEAC=8;MLEAF=1.00;MQ=50.86;MQ0=1;MQRankSum=-0.625;QD=31.98;ReadPosRankSum=0.914 GT:AD:DP:GQ:PL 1/1:0,28:28:81:913,81,0 1/1:1,38:39:99:1242,111,0 1/1:0,37:37:99:1228,108,0 1/1:1,40:41:99:1280,114,0 1 783304 . T C 4368.35 PASS AC=8;AF=1.00;AN=8;DP=135;Dels=0.00;FS=0.000;HaplotypeScore=0.6338;MLEAC=8;MLEAF=1.00;MQ=38.54;MQ0=2;QD=32.36 GT:AD:DP:GQ:PL 1/1:0,27:27:75:851,75,0 1/1:0,34:34:93:1035,93,0 1/1:0,38:38:99:1299,114,0 1/1:0,36:36:99:1209,108,0 1 785050 . G A 4332.35 PASS AC=8;AF=1.00;AN=8;DP=128;Dels=0.00;FS=0.000;HaplotypeScore=1.4686;MLEAC=8;MLEAF=1.00;MQ=58.86;MQ0=0;QD=33.85 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1134,99,0 1/1:0,31:31:90:1023,90,0 1/1:0,26:26:78:894,78,0 1/1:0,38:38:99:1307,114,0 1 785989 . T C 3348.35 PASS AC=8;AF=1.00;AN=8;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=1.0061;MLEAC=8;MLEAF=1.00;MQ=55.99;MQ0=0;QD=32.51 GT:AD:DP:GQ:PL 1/1:0,13:13:39:442,39,0 1/1:0,30:30:87:966,87,0 1/1:0,31:31:93:1045,93,0 1/1:0,29:29:81:921,81,0 1 786247 . G A 1240.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=0.000;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.3670;MLEAC=8;MLEAF=1.00;MQ=29.62;MQ0=15;MQRankSum=1.575;QD=21.02;ReadPosRankSum=0.551 GT:AD:DP:GQ:PL 1/1:3,13:16:27:270,27,0 1/1:2,11:13:30:310,30,0 1/1:2,14:16:36:393,36,0 1/1:2,12:14:30:293,30,0 1 786810 . G A 369.75 HARD_TO_VALIDATE AC=6;AF=1.00;AN=6;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=25.05;MQ0=10;QD=16.08 GT:AD:DP:GQ:PL ./. 1/1:0,5:5:9:100,9,0 1/1:0,12:12:18:202,18,0 1/1:0,6:6:9:93,9,0 1 787019 . C T 512.96 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=27.82;MQ0=11;QD=17.10 GT:AD:DP:GQ:PL 1/1:0,6:6:6:70,6,0 1/1:0,9:9:15:178,15,0 1/1:0,4:4:6:70,6,0 1/1:0,11:11:18:220,18,0 1 787070 . A G 530.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-4.783;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.3681;MLEAC=4;MLEAF=0.500;MQ=33.15;MQ0=7;MQRankSum=-0.686;QD=10.02;ReadPosRankSum=-1.317 GT:AD:DP:GQ:PL 0/1:5,4:9:79:96,0,79 0/1:6,7:13:97:167,0,97 0/1:5,8:13:82:88,0,82 0/1:7,11:18:99:212,0,126 1 787135 . A G 1560.36 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.3943;MLEAC=8;MLEAF=1.00;MQ=31.66;MQ0=7;QD=24.77 GT:AD:DP:GQ:PL 1/1:0,13:13:27:309,27,0 1/1:0,18:18:39:446,39,0 1/1:0,16:16:36:399,36,0 1/1:0,16:16:39:432,39,0 1 787185 . G A 1075.38 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.3670;MLEAC=8;MLEAF=1.00;MQ=27.61;MQ0=10;QD=19.55 GT:AD:DP:GQ:PL 1/1:0,20:20:39:427,39,0 1/1:0,13:13:21:233,21,0 1/1:0,9:9:18:199,18,0 1/1:0,12:13:24:242,24,0 1 787205 . G A 1339.37 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.2489;MLEAC=8;MLEAF=1.00;MQ=29.34;MQ0=10;QD=22.32 GT:AD:DP:GQ:PL 1/1:0,21:21:42:468,42,0 1/1:0,13:13:30:323,30,0 1/1:0,11:11:18:202,18,0 1/1:0,15:15:36:372,36,0 1 787262 . C G 2584.35 PASS AC=8;AF=1.00;AN=8;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=42.39;MQ0=5;QD=28.09 GT:AD:DP:GQ:PL 1/1:0,22:22:66:738,66,0 1/1:0,21:21:51:560,51,0 1/1:0,26:26:60:671,60,0 1/1:0,23:23:57:641,57,0 1 787399 . G T 3114.35 PASS AC=8;AF=1.00;AN=8;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=0.9305;MLEAC=8;MLEAF=1.00;MQ=50.85;MQ0=0;QD=31.14 GT:AD:DP:GQ:PL 1/1:0,21:21:60:686,60,0 1/1:0,27:27:72:810,72,0 1/1:0,19:19:54:626,54,0 1/1:0,33:33:90:1018,90,0 1 787685 . G T 4651.35 PASS AC=8;AF=1.00;AN=8;DP=145;Dels=0.00;FS=0.000;HaplotypeScore=1.4084;MLEAC=8;MLEAF=1.00;MQ=46.47;MQ0=0;QD=32.08 GT:AD:DP:GQ:PL 1/1:0,34:34:93:1064,93,0 1/1:0,31:31:90:983,90,0 1/1:0,42:42:99:1421,126,0 1/1:0,37:38:99:1209,108,0 1 787844 . C T 4315.35 PASS AC=8;AF=1.00;AN=8;DP=139;Dels=0.00;FS=0.000;HaplotypeScore=0.4987;MLEAC=8;MLEAF=1.00;MQ=39.47;MQ0=4;QD=31.05 GT:AD:DP:GQ:PL 1/1:0,33:33:90:1014,90,0 1/1:0,33:33:87:976,87,0 1/1:0,34:34:99:1150,102,0 1/1:0,38:38:99:1201,108,0 1 788713 . T C 2504.35 PASS AC=8;AF=1.00;AN=8;DP=87;Dels=0.00;FS=0.000;HaplotypeScore=0.1972;MLEAC=8;MLEAF=1.00;MQ=38.89;MQ0=4;QD=28.79 GT:AD:DP:GQ:PL 1/1:0,18:18:42:480,42,0 1/1:0,24:24:60:672,60,0 1/1:0,22:22:57:650,57,0 1/1:0,23:23:66:728,66,0 1 788840 . T C 288.58 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-3.252;DP=138;Dels=0.00;FS=15.595;HaplotypeScore=3.0085;MLEAC=4;MLEAF=0.500;MQ=30.24;MQ0=23;MQRankSum=-3.153;QD=2.09;ReadPosRankSum=1.113 GT:AD:DP:GQ:PL 0/1:16,14:33:99:169,0,184 0/1:19,20:39:99:108,0,385 0/1:19,17:37:6:6,0,417 0/1:17,11:29:37:37,0,254 1 788844 . C G 380.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-2.837;DP=143;Dels=0.00;FS=21.049;HaplotypeScore=3.0085;MLEAC=4;MLEAF=0.500;MQ=30.26;MQ0=23;MQRankSum=-2.077;QD=2.66;ReadPosRankSum=-0.532 GT:AD:DP:GQ:PL 0/1:22,11:34:99:196,0,336 0/1:28,12:40:93:93,0,512 0/1:23,16:39:44:44,0,446 0/1:20,10:30:80:80,0,289 1 789099 . G A 922.84 HARD_TO_VALIDATE AC=7;AF=0.875;AN=8;BaseQRankSum=3.014;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7110;MLEAC=7;MLEAF=0.875;MQ=27.39;MQ0=12;MQRankSum=0.843;QD=15.13;ReadPosRankSum=0.586 GT:AD:DP:GQ:PL 1/1:3,12:15:1:282,1,0 1/1:2,17:19:36:379,36,0 0/1:7,10:17:41:57,0,41 1/1:2,8:10:5:234,5,0 1 789141 . G C 884.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.166;DP=166;Dels=0.00;FS=3.137;HaplotypeScore=1.1444;MLEAC=4;MLEAF=0.500;MQ=30.28;MQ0=29;MQRankSum=3.597;QD=5.33;ReadPosRankSum=-2.691 GT:AD:DP:GQ:PL 0/1:29,17:46:99:379,0,448 0/1:34,7:41:58:58,0,603 0/1:26,16:42:99:287,0,362 0/1:28,9:37:99:193,0,476 1 789242 . C G 49.90 LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-3.508;DP=124;Dels=0.00;FS=35.198;HaplotypeScore=4.8477;MLEAC=2;MLEAF=0.250;MQ=39.09;MQ0=7;MQRankSum=0.076;QD=0.86;ReadPosRankSum=-4.272 GT:AD:DP:GQ:PL 0/1:26,5:31:40:40,0,420 0/0:37,1:38:60:0,60,865 0/0:27,1:28:57:0,57,617 0/1:21,6:27:44:44,0,293 1 789256 . T C 2491.35 PASS AC=8;AF=1.00;AN=8;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=1.0106;MLEAC=8;MLEAF=1.00;MQ=41.37;MQ0=5;QD=20.94 GT:AD:DP:GQ:PL 1/1:0,30:30:63:613,63,0 1/1:0,37:37:87:862,87,0 1/1:0,30:31:63:652,63,0 1/1:0,21:21:39:390,39,0 1 789465 . C T 1960.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.886;DP=172;Dels=0.00;FS=0.604;HaplotypeScore=0.4138;MLEAC=4;MLEAF=0.500;MQ=32.48;MQ0=23;MQRankSum=-1.166;QD=11.40;ReadPosRankSum=-1.078 GT:AD:DP:GQ:PL 0/1:17,23:40:99:571,0,302 0/1:26,27:53:99:542,0,431 0/1:24,19:43:99:398,0,602 0/1:14,21:35:99:482,0,255 1 792263 . A G 3847.35 PASS AC=8;AF=1.00;AN=8;DP=142;Dels=0.00;FS=0.000;HaplotypeScore=0.4771;MLEAC=8;MLEAF=1.00;MQ=41.20;MQ0=4;QD=27.09 GT:AD:DP:GQ:PL 1/1:0,36:36:90:984,90,0 1/1:0,28:28:84:878,84,0 1/1:1,40:41:99:1079,105,0 1/1:1,36:37:93:932,93,0 1 792480 . C T 5178.35 PASS AC=8;AF=1.00;AN=8;DP=164;Dels=0.00;FS=0.000;HaplotypeScore=0.8721;MLEAC=8;MLEAF=1.00;MQ=44.96;MQ0=2;QD=31.58 GT:AD:DP:GQ:PL 1/1:0,30:30:90:1017,90,0 1/1:0,47:47:99:1400,126,0 1/1:0,42:42:99:1294,114,0 1/1:0,45:45:99:1493,135,0 1 793208 . C G 234.10 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=1.402;DP=51;Dels=0.00;FS=33.294;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=25.63;MQ0=11;MQRankSum=3.911;QD=4.59;ReadPosRankSum=-3.527 GT:AD:DP:GQ:PL 0/1:7,1:8:21:21,0,111 0/1:8,7:15:99:105,0,188 0/1:12,9:21:99:127,0,229 0/1:6,1:7:13:13,0,83 1 793393 . A G 262.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-4.563;DP=86;Dels=0.00;FS=5.456;HaplotypeScore=0.4989;MLEAC=4;MLEAF=0.500;MQ=25.24;MQ0=40;MQRankSum=4.105;QD=3.06;ReadPosRankSum=1.120 GT:AD:DP:GQ:PL 0/1:10,4:14:74:74,0,112 0/1:21,7:28:84:84,0,281 0/1:13,7:20:83:83,0,167 0/1:19,4:23:54:54,0,200 1 793429 . T C 1025.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-0.352;DP=95;Dels=0.00;FS=3.687;HaplotypeScore=0.9971;MLEAC=4;MLEAF=0.500;MQ=27.65;MQ0=37;MQRankSum=2.642;QD=10.80;ReadPosRankSum=-0.417 GT:AD:DP:GQ:PL 0/1:9,3:12:49:49,0,146 0/1:10,22:32:99:472,0,158 0/1:8,17:25:59:306,0,59 0/1:15,11:26:92:231,0,92 1 793507 . T C 44.38 LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=2.568;DP=97;Dels=0.00;FS=11.205;HaplotypeScore=0.5058;MLEAC=1;MLEAF=0.125;MQ=44.17;MQ0=8;MQRankSum=-2.233;QD=2.22;ReadPosRankSum=-1.958 GT:AD:DP:GQ:PL 0/1:16,4:20:76:76,0,460 0/0:29,2:31:44:0,44,812 0/0:23,1:24:17:0,17,489 0/0:18,4:22:45:0,45,497 1 793750 . G T 257.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.165;DP=157;Dels=0.00;FS=7.645;HaplotypeScore=1.3263;MLEAC=4;MLEAF=0.500;MQ=53.32;MQ0=2;MQRankSum=-8.372;QD=1.64;ReadPosRankSum=0.070 GT:AD:DP:GQ:PL 0/1:30,8:38:61:61,0,858 0/1:41,9:50:80:80,0,1192 0/1:28,7:35:90:90,0,842 0/1:26,8:34:59:59,0,763 1 796643 . C T 308.35 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=0.431;DP=173;Dels=0.00;FS=47.967;HaplotypeScore=1.0711;MLEAC=4;MLEAF=0.500;MQ=30.35;MQ0=50;MQRankSum=-3.470;QD=1.78;ReadPosRankSum=-1.839 GT:AD:DP:GQ:PL 0/1:34,11:45:99:151,0,573 0/1:40,9:49:66:66,0,859 0/1:33,9:42:8:8,0,791 0/1:28,9:37:99:115,0,596 1 796727 . G T 1849.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=5.694;DP=169;Dels=0.01;FS=15.992;HaplotypeScore=1.6915;MLEAC=4;MLEAF=0.500;MQ=39.64;MQ0=18;MQRankSum=-5.796;QD=10.95;ReadPosRankSum=-1.410 GT:AD:DP:GQ:PL 0/1:27,25:52:99:382,0,684 0/1:15,25:40:99:547,0,320 0/1:12,26:38:99:647,0,132 0/1:21,16:37:99:306,0,473 1 796767 . G A 3015.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.576;DP=212;Dels=0.00;FS=1.779;HaplotypeScore=3.6355;MLEAC=4;MLEAF=0.500;MQ=41.24;MQ0=15;MQRankSum=-8.168;QD=14.23;ReadPosRankSum=0.666 GT:AD:DP:GQ:PL 0/1:25,34:59:99:706,0,662 0/1:16,34:50:99:857,0,407 0/1:14,33:47:99:874,0,311 0/1:28,26:54:99:611,0,753 1 796775 . T C 2055.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.932;DP=218;Dels=0.00;FS=4.096;HaplotypeScore=2.1009;MLEAC=4;MLEAF=0.500;MQ=40.71;MQ0=17;MQRankSum=7.855;QD=9.43;ReadPosRankSum=-1.205 GT:AD:DP:GQ:PL 0/1:38,26:64:99:676,0,762 0/1:33,15:48:99:362,0,815 0/1:36,13:49:99:300,0,946 0/1:29,28:57:99:750,0,621 1 796848 . A T 1053.95 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=2.960;DP=183;Dels=0.00;FS=8.603;HaplotypeScore=1.5181;MLEAC=4;MLEAF=0.500;MQ=33.58;MQ0=36;MQRankSum=0.040;QD=5.76;ReadPosRankSum=-0.579 GT:AD:DP:GQ:PL 0/1:30,19:49:99:375,0,567 0/1:40,5:45:33:33,0,832 0/1:30,12:42:99:229,0,741 0/1:29,18:47:99:449,0,620 1 798026 . C T 4847.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.686;DP=154;Dels=0.00;FS=0.000;HaplotypeScore=0.6918;MLEAC=8;MLEAF=1.00;MQ=43.20;MQ0=3;MQRankSum=0.883;QD=31.48;ReadPosRankSum=-0.241 GT:AD:DP:GQ:PL 1/1:0,37:37:99:1126,99,0 1/1:0,36:36:93:1063,93,0 1/1:1,31:32:93:1093,93,0 1/1:1,48:49:99:1591,138,0 1 799463 . T C 5508.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.672;DP=172;Dels=0.00;FS=0.000;HaplotypeScore=1.4334;MLEAC=8;MLEAF=1.00;MQ=58.42;MQ0=0;MQRankSum=1.631;QD=32.03;ReadPosRankSum=-1.329 GT:AD:DP:GQ:PL 1/1:1,36:37:99:1171,105,0 1/1:0,51:51:99:1658,153,0 1/1:0,54:54:99:1773,159,0 1/1:0,30:30:84:932,84,0 1 800007 . T C 5259.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.644;DP=160;Dels=0.00;FS=3.239;HaplotypeScore=1.4593;MLEAC=8;MLEAF=1.00;MQ=49.64;MQ0=2;MQRankSum=0.110;QD=32.87;ReadPosRankSum=1.579 GT:AD:DP:GQ:PL 1/1:0,34:34:96:1093,96,0 1/1:0,32:32:90:1021,90,0 1/1:0,38:38:99:1304,114,0 1/1:1,55:56:99:1867,138,0 1 800383 . C T 4448.35 PASS AC=8;AF=1.00;AN=8;DP=133;Dels=0.00;FS=0.000;HaplotypeScore=0.6749;MLEAC=8;MLEAF=1.00;MQ=41.77;MQ0=2;QD=33.45 GT:AD:DP:GQ:PL 1/1:0,33:33:90:1007,90,0 1/1:0,30:30:90:1033,90,0 1/1:0,37:37:99:1297,111,0 1/1:0,33:33:99:1137,99,0 1 801943 . C T 5456.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=0.764;DP=201;Dels=0.00;FS=0.000;HaplotypeScore=1.7830;MLEAC=8;MLEAF=1.00;MQ=47.22;MQ0=9;MQRankSum=1.979;QD=27.15;ReadPosRankSum=1.246 GT:AD:DP:GQ:PL 1/1:1,52:53:99:1375,126,0 1/1:2,63:65:99:1820,168,0 1/1:1,46:47:99:1222,111,0 1/1:0,36:36:96:1065,96,0 1 802006 . T C 1019.73 HARD_TO_VALIDATE AC=5;AF=0.625;AN=8;BaseQRankSum=0.922;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=0.8675;MLEAC=5;MLEAF=0.625;MQ=23.02;MQ0=39;MQRankSum=2.345;QD=8.64;ReadPosRankSum=-0.365 GT:AD:DP:GQ:PL 0/1:7,24:32:21:331,0,21 1/1:7,31:38:45:462,45,0 0/1:8,16:24:7:141,0,7 0/1:10,14:24:78:119,0,78 1 802093 . G A 1921.99 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;BaseQRankSum=4.761;DP=192;Dels=0.00;FS=13.460;HaplotypeScore=2.5518;MLEAC=8;MLEAF=1.00;MQ=20.97;MQ0=42;MQRankSum=3.388;QD=10.01;ReadPosRankSum=2.215 GT:AD:DP:GQ:PL 1/1:6,42:51:57:568,57,0 1/1:15,34:49:2:386,2,0 1/1:6,37:43:45:466,45,0 1/1:9,40:49:51:527,51,0 1 802104 . T C 167.91 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.374;DP=180;Dels=0.00;FS=7.815;HaplotypeScore=1.8710;MLEAC=3;MLEAF=0.375;MQ=21.28;MQ0=32;MQRankSum=0.698;QD=1.23;ReadPosRankSum=0.889 GT:AD:DP:GQ:PL 0/1:33,19:53:99:115,0,353 0/0:38,6:44:42:0,42,419 0/1:34,6:40:55:55,0,319 0/1:29,14:43:32:32,0,355 1 802124 . G A 43.41 HARD_TO_VALIDATE;LowQD;LowQual AC=3;AF=0.375;AN=8;BaseQRankSum=3.140;DP=220;Dels=0.00;FS=45.830;HaplotypeScore=3.5470;MLEAC=3;MLEAF=0.375;MQ=18.55;MQ0=30;MQRankSum=0.303;QD=0.26;ReadPosRankSum=-0.446 GT:AD:DP:GQ:PL 0/1:60,8:69:16:16,0,465 0/0:48,5:54:13:0,13,418 0/1:36,4:41:18:18,0,347 0/1:43,9:56:43:43,0,359 1 802191 . G A 242.93 HARD_TO_VALIDATE;LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=3.190;DP=489;Dels=0.00;FS=26.992;HaplotypeScore=5.0006;MLEAC=3;MLEAF=0.375;MQ=12.55;MQ0=127;MQRankSum=-1.072;QD=0.61;ReadPosRankSum=-2.771 GT:AD:DP:GQ:PL 0/1:123,33:161:46:46,0,461 0/1:90,44:135:99:101,0,619 0/1:71,29:101:99:130,0,425 0/0:74,18:92:25:0,25,512 1 802240 . G A 444.94 HARD_TO_VALIDATE;LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=4.361;DP=409;Dels=0.00;FS=3.661;HaplotypeScore=13.8502;MLEAC=4;MLEAF=0.500;MQ=11.67;MQ0=126;MQRankSum=2.054;QD=1.09;ReadPosRankSum=-1.825 GT:AD:DP:GQ:PL 0/1:95,36:137:63:63,0,197 0/1:74,29:105:99:151,0,203 0/1:63,26:89:99:159,0,200 0/1:62,16:78:99:104,0,139 1 802320 . G A 2466.31 HARD_TO_VALIDATE AC=6;AF=0.750;AN=8;BaseQRankSum=4.747;DP=235;Dels=0.00;FS=35.854;HaplotypeScore=4.1652;MLEAC=7;MLEAF=0.875;MQ=30.48;MQ0=29;MQRankSum=6.253;QD=10.49;ReadPosRankSum=2.529 GT:AD:DP:GQ:PL 0/1:26,46:75:99:652,0,116 1/1:19,41:61:17:878,17,0 1/1:21,29:51:15:563,15,0 0/1:19,26:47:2:404,0,2 1 802338 . G A 71.84 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=4.885;DP=252;Dels=0.00;FS=4.009;HaplotypeScore=3.4475;MLEAC=2;MLEAF=0.250;MQ=33.47;MQ0=33;MQRankSum=-6.852;QD=0.51;ReadPosRankSum=0.126 GT:AD:DP:GQ:PL 0/1:62,20:84:57:57,0,916 0/0:46,16:63:4:0,4,795 0/1:35,22:57:47:47,0,556 0/0:30,18:48:10:0,10,446 1 802381 . T C 100.92 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.724;DP=247;Dels=0.00;FS=10.985;HaplotypeScore=5.8982;MLEAC=3;MLEAF=0.375;MQ=41.23;MQ0=21;MQRankSum=-8.977;QD=0.51;ReadPosRankSum=2.588 GT:AD:DP:GQ:PL 0/1:48,34:82:82:82,0,1014 0/1:50,22:72:21:21,0,1157 0/1:27,17:45:31:31,0,479 0/0:30,18:48:8:0,8,705 1 804115 . G A 3168.35 HARD_TO_VALIDATE AC=8;AF=1.00;AN=8;DP=122;Dels=0.01;FS=0.000;HaplotypeScore=0.8149;MLEAC=8;MLEAF=1.00;MQ=32.50;MQ0=13;QD=25.97 GT:AD:DP:GQ:PL 1/1:0,31:31:87:931,87,0 1/1:0,32:32:75:806,75,0 1/1:0,25:25:54:564,54,0 1/1:0,33:33:87:893,87,0 1 804540 . T C 3514.35 PASS AC=8;AF=1.00;AN=8;DP=128;Dels=0.00;FS=0.000;HaplotypeScore=1.2036;MLEAC=8;MLEAF=1.00;MQ=54.25;MQ0=0;QD=27.46 GT:AD:DP:GQ:PL 1/1:0,26:27:60:653,60,0 1/1:0,40:40:99:1188,117,0 1/1:0,29:29:72:798,72,0 1/1:0,32:32:90:901,90,0 1 807512 . A G 3628.35 PASS AC=8;AF=1.00;AN=8;DP=108;Dels=0.00;FS=0.000;HaplotypeScore=0.1835;MLEAC=8;MLEAF=1.00;MQ=51.93;MQ0=0;QD=33.60 GT:AD:DP:GQ:PL 1/1:0,12:12:36:417,36,0 1/1:0,30:30:90:1025,90,0 1/1:0,31:31:90:1034,90,0 1/1:0,35:35:99:1178,105,0 1 807761 . C A 4326.35 PASS AC=8;AF=1.00;AN=8;DP=132;Dels=0.00;FS=0.000;HaplotypeScore=0.6692;MLEAC=8;MLEAF=1.00;MQ=56.39;MQ0=0;QD=32.78 GT:AD:DP:GQ:PL 1/1:0,30:30:84:998,84,0 1/1:0,32:32:96:1081,96,0 1/1:0,37:37:99:1151,99,0 1/1:0,33:33:99:1122,99,0 1 808223 . G C 2815.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=0.779;DP=146;Dels=0.00;FS=4.743;HaplotypeScore=2.3492;MLEAC=8;MLEAF=1.00;MQ=38.40;MQ0=6;MQRankSum=1.669;QD=19.28;ReadPosRankSum=-0.172 GT:AD:DP:GQ:PL 1/1:6,32:38:57:736,57,0 1/1:5,28:33:38:573,38,0 1/1:2,33:36:84:791,84,0 1/1:3,34:39:78:741,78,0 1 808631 . G A 5709.35 PASS AC=8;AF=1.00;AN=8;DP=168;Dels=0.00;FS=0.000;HaplotypeScore=0.5777;MLEAC=8;MLEAF=1.00;MQ=57.30;MQ0=0;QD=33.98 GT:AD:DP:GQ:PL 1/1:0,48:48:99:1660,144,0 1/1:0,52:52:99:1771,156,0 1/1:0,31:31:93:1054,93,0 1/1:0,37:37:99:1250,108,0 1 808922 . G A 4842.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=2.046;DP=161;Dels=0.00;FS=2.053;HaplotypeScore=1.8536;MLEAC=8;MLEAF=1.00;MQ=44.59;MQ0=2;MQRankSum=2.416;QD=30.08;ReadPosRankSum=-1.587 GT:AD:DP:GQ:PL 1/1:0,41:43:99:1168,102,0 1/1:3,52:55:92:1668,92,0 1/1:3,29:32:65:964,65,0 1/1:0,31:31:93:1068,93,0 1 808928 . C T 4981.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=3.331;DP=164;Dels=0.00;FS=0.000;HaplotypeScore=2.1898;MLEAC=8;MLEAF=1.00;MQ=45.32;MQ0=2;MQRankSum=2.469;QD=30.37;ReadPosRankSum=-1.714 GT:AD:DP:GQ:PL 1/1:0,45:45:99:1369,120,0 1/1:4,48:52:78:1537,78,0 1/1:3,32:35:45:1003,45,0 1/1:0,32:32:96:1098,96,0 1 811523 . G C 34.33 LowQual AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=2.3779;MLEAC=2;MLEAF=1.00;MQ=22.79;MQ0=0;QD=11.44 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:3:6:59,6,0 ./. 1 811765 . C T 249.76 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.338;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=3.3614;MLEAC=5;MLEAF=0.625;MQ=42.89;MQ0=2;MQRankSum=2.281;QD=9.61;ReadPosRankSum=-0.375 GT:AD:DP:GQ:PL 0/1:4,1:5:20:20,0,26 0/1:7,5:13:31:110,0,31 0/0:1,0:1:3:0,3,29 1/1:2,6:8:15:154,15,0 1 812267 . A G 4127.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=-0.601;DP=144;Dels=0.00;FS=0.000;HaplotypeScore=0.7788;MLEAC=8;MLEAF=1.00;MQ=53.60;MQ0=0;MQRankSum=0.674;QD=28.66;ReadPosRankSum=-1.564 GT:AD:DP:GQ:PL 1/1:0,33:33:90:943,90,0 1/1:0,37:37:99:1123,108,0 1/1:0,38:38:99:1135,111,0 1/1:1,35:36:66:952,66,0 1 812284 . C G 4278.42 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=1.096;DP=139;Dels=0.00;FS=12.308;HaplotypeScore=1.2249;MLEAC=8;MLEAF=1.00;MQ=53.39;MQ0=1;MQRankSum=3.667;QD=30.78;ReadPosRankSum=3.564 GT:AD:DP:GQ:PL 1/1:3,29:32:12:858,12,0 1/1:3,37:40:59:1192,59,0 1/1:0,31:31:90:1027,90,0 1/1:0,36:36:99:1227,108,0 1 812751 . T C 4806.35 PASS AC=8;AF=1.00;AN=8;DP=149;Dels=0.00;FS=0.000;HaplotypeScore=1.3356;MLEAC=8;MLEAF=1.00;MQ=58.32;MQ0=6;QD=32.26 GT:AD:DP:GQ:PL 1/1:0,33:33:93:1083,93,0 1/1:0,39:39:99:1322,114,0 1/1:0,35:35:93:1062,93,0 1/1:0,42:42:99:1365,120,0 1 813046 . G A 206.04 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-1.621;DP=196;Dels=0.00;FS=45.600;HaplotypeScore=3.2689;MLEAC=3;MLEAF=0.375;MQ=55.05;MQ0=2;MQRankSum=-9.272;QD=1.40;ReadPosRankSum=-6.063 GT:AD:DP:GQ:PL 0/0:41,8:49:24:0,24,1227 0/1:44,7:51:16:16,0,1343 0/1:35,10:45:99:100,0,1069 0/1:37,14:51:99:124,0,1114 1 813050 . G A 415.67 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.965;DP=206;Dels=0.00;FS=58.563;HaplotypeScore=3.3115;MLEAC=4;MLEAF=0.500;MQ=54.58;MQ0=2;MQRankSum=-10.108;QD=2.02;ReadPosRankSum=-4.908 GT:AD:DP:GQ:PL 0/1:41,9:50:6:6,0,1223 0/1:46,7:53:15:15,0,1399 0/1:34,12:46:99:167,0,992 0/1:38,19:57:99:259,0,1082 1 813067 . T C 1306.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-6.317;DP=231;Dels=0.00;FS=95.344;HaplotypeScore=2.2640;MLEAC=4;MLEAF=0.500;MQ=50.15;MQ0=4;MQRankSum=-12.391;QD=5.66;ReadPosRankSum=-2.322 GT:AD:DP:GQ:PL 0/1:38,19:57:99:217,0,1126 0/1:42,19:62:99:196,0,1286 0/1:31,20:51:99:364,0,958 0/1:28,32:61:99:562,0,795 1 813089 . G A 181.09 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-2.956;DP=269;Dels=0.00;FS=31.765;HaplotypeScore=3.2728;MLEAC=2;MLEAF=0.250;MQ=49.05;MQ0=11;MQRankSum=-6.110;QD=1.36;ReadPosRankSum=3.047 GT:AD:DP:GQ:PL 0/1:50,10:60:16:16,0,1312 0/0:67,5:72:74:0,74,1675 0/0:58,5:64:50:0,50,1622 0/1:56,16:73:99:199,0,1396 1 813109 . A C 1544.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.678;DP=266;Dels=0.00;FS=138.432;HaplotypeScore=3.1622;MLEAC=4;MLEAF=0.500;MQ=49.13;MQ0=10;MQRankSum=-13.542;QD=5.81;ReadPosRankSum=5.739 GT:AD:DP:GQ:PL 0/1:32,28:60:99:354,0,961 0/1:47,26:73:99:244,0,1343 0/1:40,22:62:99:403,0,1212 0/1:35,36:71:99:576,0,974 1 813112 . T C 1426.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=8.086;DP=276;Dels=0.00;FS=147.958;HaplotypeScore=2.9925;MLEAC=4;MLEAF=0.500;MQ=48.30;MQ0=13;MQRankSum=-12.765;QD=5.17;ReadPosRankSum=5.328 GT:AD:DP:GQ:PL 0/1:36,27:63:99:327,0,835 0/1:52,26:78:99:184,0,1345 0/1:40,22:62:99:406,0,1135 0/1:36,37:73:99:542,0,887 1 813237 . T C 42.53 LowQD;LowQual AC=1;AF=0.125;AN=8;BaseQRankSum=0.531;DP=216;Dels=0.00;FS=1.012;HaplotypeScore=1.7460;MLEAC=1;MLEAF=0.125;MQ=44.78;MQ0=13;MQRankSum=-8.844;QD=0.75;ReadPosRankSum=-0.916 GT:AD:DP:GQ:PL 0/0:48,13:61:25:0,25,1421 0/0:45,13:58:73:0,73,1445 0/1:46,11:57:74:74,0,1398 0/0:28,11:39:11:0,11,840 1 813246 . G A 79.54 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-2.804;DP=224;Dels=0.00;FS=0.882;HaplotypeScore=2.3334;MLEAC=2;MLEAF=0.250;MQ=45.34;MQ0=14;MQRankSum=-9.524;QD=0.77;ReadPosRankSum=-0.079 GT:AD:DP:GQ:PL 0/0:49,15:64:6:0,6,1430 0/0:45,12:57:24:0,24,1408 0/1:48,12:60:99:102,0,1426 0/1:30,13:43:10:10,0,933 1 813250 . G T 257.37 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=1.697;DP=224;Dels=0.00;FS=1.771;HaplotypeScore=1.5870;MLEAC=3;MLEAF=0.375;MQ=45.10;MQ0=13;MQRankSum=-10.204;QD=1.51;ReadPosRankSum=-1.200 GT:AD:DP:GQ:PL 0/1:48,18:66:99:102,0,1441 0/0:41,13:54:6:0,6,1210 0/1:47,14:61:99:110,0,1415 0/1:29,14:43:78:78,0,851 1 813288 . G T 1183.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.335;DP=237;Dels=0.00;FS=0.000;HaplotypeScore=2.6595;MLEAC=4;MLEAF=0.500;MQ=46.34;MQ0=12;MQRankSum=-12.139;QD=5.00;ReadPosRankSum=0.494 GT:AD:DP:GQ:PL 0/1:39,29:68:99:317,0,1169 0/1:37,26:63:99:289,0,1058 0/1:40,17:57:99:250,0,1221 0/1:28,21:49:99:360,0,798 1 813291 . A G 1131.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.186;DP=232;Dels=0.00;FS=0.000;HaplotypeScore=2.1600;MLEAC=4;MLEAF=0.500;MQ=47.18;MQ0=12;MQRankSum=-12.013;QD=4.88;ReadPosRankSum=1.547 GT:AD:DP:GQ:PL 0/1:39,26:66:99:286,0,1190 0/1:38,22:61:99:262,0,1113 0/1:37,19:56:99:259,0,1117 0/1:28,21:49:99:357,0,772 1 813317 . C A 1235.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=9.422;DP=251;Dels=0.00;FS=9.869;HaplotypeScore=5.6966;MLEAC=4;MLEAF=0.500;MQ=47.52;MQ0=12;MQRankSum=-12.380;QD=4.92;ReadPosRankSum=4.290 GT:AD:DP:GQ:PL 0/1:43,28:71:99:283,0,1176 0/1:39,23:62:99:234,0,1025 0/1:36,20:56:99:281,0,964 0/1:34,28:62:99:470,0,837 1 813331 . G T 1138.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-2.107;DP=256;Dels=0.00;FS=15.400;HaplotypeScore=1.4721;MLEAC=4;MLEAF=0.500;MQ=45.70;MQ0=16;MQRankSum=-12.282;QD=4.45;ReadPosRankSum=3.194 GT:AD:DP:GQ:PL 0/1:39,30:69:99:285,0,1153 0/1:45,21:66:99:185,0,1293 0/1:36,20:56:99:246,0,1097 0/1:35,30:65:99:455,0,1008 1 813340 . G A 788.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.110;DP=241;Dels=0.00;FS=7.111;HaplotypeScore=1.1497;MLEAC=4;MLEAF=0.500;MQ=46.19;MQ0=12;MQRankSum=-11.546;QD=3.27;ReadPosRankSum=3.225 GT:AD:DP:GQ:PL 0/1:39,24:63:99:173,0,1131 0/1:43,19:62:99:171,0,1213 0/1:40,15:55:99:163,0,1229 0/1:37,24:61:99:314,0,1040 1 813341 . C T 827.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.620;DP=242;Dels=0.00;FS=7.016;HaplotypeScore=1.1497;MLEAC=4;MLEAF=0.500;MQ=46.10;MQ0=11;MQRankSum=-11.268;QD=3.42;ReadPosRankSum=3.099 GT:AD:DP:GQ:PL 0/1:41,23:64:99:171,0,1183 0/1:42,19:61:99:175,0,1198 0/1:41,15:56:99:165,0,1241 0/1:36,25:61:99:349,0,1056 1 813342 . A G 819.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-2.358;DP=241;Dels=0.00;FS=8.133;HaplotypeScore=1.3993;MLEAC=4;MLEAF=0.500;MQ=45.80;MQ0=11;MQRankSum=-11.425;QD=3.40;ReadPosRankSum=2.495 GT:AD:DP:GQ:PL 0/1:39,24:63:99:169,0,1179 0/1:42,19:61:99:172,0,1238 0/1:40,15:55:99:167,0,1246 0/1:37,25:62:99:344,0,1051 1 813353 . C A 230.21 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=0.119;DP=257;Dels=0.00;FS=2.681;HaplotypeScore=2.4749;MLEAC=3;MLEAF=0.375;MQ=43.56;MQ0=13;MQRankSum=-6.722;QD=1.18;ReadPosRankSum=-1.259 GT:AD:DP:GQ:PL 0/1:52,11:63:14:14,0,1269 0/1:58,9:67:59:59,0,1414 0/0:56,6:62:17:0,17,1535 0/1:50,15:65:99:191,0,1244 1 813377 . G T 979.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.272;DP=265;Dels=0.00;FS=43.878;HaplotypeScore=2.4684;MLEAC=4;MLEAF=0.500;MQ=42.05;MQ0=13;MQRankSum=-12.105;QD=3.70;ReadPosRankSum=-4.042 GT:AD:DP:GQ:PL 0/1:40,25:65:56:56,0,1251 0/1:49,23:72:99:204,0,1405 0/1:40,24:64:99:367,0,1170 0/1:32,32:64:99:385,0,930 1 813385 . G T 836.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.823;DP=270;Dels=0.00;FS=45.943;HaplotypeScore=1.3299;MLEAC=4;MLEAF=0.500;MQ=43.04;MQ0=13;MQRankSum=-11.878;QD=3.10;ReadPosRankSum=-0.659 GT:AD:DP:GQ:PL 0/1:43,20:63:51:51,0,1299 0/1:50,26:76:99:227,0,1478 0/1:43,22:65:99:273,0,1254 0/1:37,28:65:99:318,0,1097 1 813397 . G C 774.95 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=3.823;DP=272;Dels=0.00;FS=35.010;HaplotypeScore=1.3846;MLEAC=4;MLEAF=0.500;MQ=43.26;MQ0=17;MQRankSum=-11.656;QD=2.85;ReadPosRankSum=3.338 GT:AD:DP:GQ:PL 0/1:42,22:64:25:25,0,1200 0/1:54,27:81:99:292,0,1465 0/1:42,20:62:99:266,0,1236 0/1:39,26:65:99:224,0,1101 1 813417 . G C 871.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=8.583;DP=270;Dels=0.00;FS=45.565;HaplotypeScore=8.2954;MLEAC=4;MLEAF=0.500;MQ=42.22;MQ0=23;MQRankSum=-11.893;QD=3.23;ReadPosRankSum=2.971 GT:AD:DP:GQ:PL 0/1:33,25:58:94:94,0,897 0/1:50,32:82:99:400,0,1268 0/1:48,22:70:99:224,0,1230 0/1:33,27:60:99:186,0,853 1 813421 . G A 155.90 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-3.434;DP=269;Dels=0.00;FS=44.187;HaplotypeScore=9.0369;MLEAC=3;MLEAF=0.375;MQ=42.30;MQ0=22;MQRankSum=-6.130;QD=0.75;ReadPosRankSum=0.262 GT:AD:DP:GQ:PL 0/0:50,11:61:58:0,58,1244 0/1:68,14:82:73:73,0,1718 0/1:57,10:67:53:53,0,1523 0/1:49,10:59:64:64,0,1097 1 813439 . G A 602.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.957;DP=260;Dels=0.00;FS=39.373;HaplotypeScore=5.5248;MLEAC=4;MLEAF=0.500;MQ=43.84;MQ0=24;MQRankSum=-11.740;QD=2.32;ReadPosRankSum=0.639 GT:AD:DP:GQ:PL 0/1:35,30:66:91:91,0,1013 0/1:44,30:74:99:356,0,1165 0/1:51,16:67:87:87,0,1516 0/1:31,22:53:99:101,0,924 1 813462 . T A 128.90 HARD_TO_VALIDATE;LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-1.448;DP=206;Dels=0.00;FS=31.165;HaplotypeScore=2.0187;MLEAC=2;MLEAF=0.250;MQ=48.29;MQ0=21;MQRankSum=-8.846;QD=1.15;ReadPosRankSum=3.077 GT:AD:DP:GQ:PL 0/1:33,19:52:45:45,0,963 0/1:41,18:60:99:118,0,1153 0/0:45,8:53:77:0,77,1453 0/0:31,10:41:36:0,36,963 1 813640 . A G 3887.35 PASS AC=8;AF=1.00;AN=8;DP=131;Dels=0.00;FS=0.000;HaplotypeScore=0.8565;MLEAC=8;MLEAF=1.00;MQ=37.88;MQ0=2;QD=29.67 GT:AD:DP:GQ:PL 1/1:0,33:33:93:972,93,0 1/1:0,27:27:78:805,78,0 1/1:0,29:29:84:884,84,0 1/1:0,42:42:99:1252,120,0 1 813747 . G A 4262.35 PASS AC=8;AF=1.00;AN=8;DP=132;Dels=0.00;FS=0.000;HaplotypeScore=0.8139;MLEAC=8;MLEAF=1.00;MQ=41.60;MQ0=2;QD=32.29 GT:AD:DP:GQ:PL 1/1:0,21:21:51:588,51,0 1/1:0,42:43:99:1405,126,0 1/1:0,28:28:81:923,81,0 1/1:0,40:40:99:1372,120,0 1 814052 . G A 149.71 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.016;DP=185;Dels=0.00;FS=20.134;HaplotypeScore=0.3915;MLEAC=3;MLEAF=0.375;MQ=48.08;MQ0=13;MQRankSum=-8.963;QD=0.98;ReadPosRankSum=-4.402 GT:AD:DP:GQ:PL 0/1:35,22:57:99:117,0,920 0/0:29,4:33:5:0,5,790 0/1:29,11:40:22:22,0,887 0/1:41,14:55:43:43,0,1190 1 814087 . C A 930.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=-3.843;DP=223;Dels=0.00;FS=70.524;HaplotypeScore=2.5810;MLEAC=4;MLEAF=0.500;MQ=39.02;MQ0=26;MQRankSum=-9.636;QD=4.17;ReadPosRankSum=3.592 GT:AD:DP:GQ:PL 0/1:33,38:71:99:279,0,867 0/1:32,19:51:99:337,0,803 0/1:27,17:44:99:168,0,767 0/1:35,22:57:99:179,0,935 1 814094 . A G 1235.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=3.226;DP=231;Dels=0.00;FS=94.422;HaplotypeScore=2.2486;MLEAC=4;MLEAF=0.500;MQ=37.31;MQ0=28;MQRankSum=-9.375;QD=5.35;ReadPosRankSum=3.977 GT:AD:DP:GQ:PL 0/1:29,41:72:99:289,0,725 0/1:26,24:51:99:423,0,592 0/1:28,19:47:99:264,0,737 0/1:34,27:61:99:292,0,839 1 814105 . C T 1347.94 HARD_TO_VALIDATE AC=4;AF=0.500;AN=8;BaseQRankSum=7.311;DP=234;Dels=0.00;FS=62.972;HaplotypeScore=2.4249;MLEAC=4;MLEAF=0.500;MQ=34.44;MQ0=27;MQRankSum=-8.198;QD=5.76;ReadPosRankSum=2.651 GT:AD:DP:GQ:PL 0/1:32,41:73:99:312,0,692 0/1:28,25:53:99:425,0,526 0/1:29,22:51:99:322,0,723 0/1:30,27:57:99:321,0,642 1 814147 . G C 2047.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.690;DP=238;Dels=0.00;FS=118.176;HaplotypeScore=7.7807;MLEAC=4;MLEAF=0.500;MQ=32.01;MQ0=21;MQRankSum=-7.492;QD=8.60;ReadPosRankSum=0.611 GT:AD:DP:GQ:PL 0/1:27,36:63:99:355,0,708 0/1:31,32:63:99:516,0,775 0/1:24,30:54:99:611,0,648 0/1:22,36:58:99:598,0,485 1 814157 . A G 260.05 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=-0.863;DP=232;Dels=0.00;FS=20.941;HaplotypeScore=10.6880;MLEAC=2;MLEAF=0.250;MQ=32.48;MQ0=18;MQRankSum=-1.407;QD=2.08;ReadPosRankSum=2.552 GT:AD:DP:GQ:PL 0/0:54,3:57:15:0,15,1008 0/1:54,11:65:99:114,0,1248 0/0:45,5:50:27:0,27,1262 0/1:45,15:60:99:180,0,1076 1 814160 . C G 1543.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-3.429;DP=226;Dels=0.00;FS=84.685;HaplotypeScore=10.6900;MLEAC=4;MLEAF=0.500;MQ=32.87;MQ0=16;MQRankSum=-8.136;QD=6.83;ReadPosRankSum=1.726 GT:AD:DP:GQ:PL 0/1:30,27:57:99:189,0,776 0/1:32,27:60:99:503,0,745 0/1:29,21:50:99:364,0,832 0/1:30,29:59:99:520,0,747 1 814173 . A T 1627.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.413;DP=232;Dels=0.00;FS=78.308;HaplotypeScore=4.1111;MLEAC=4;MLEAF=0.500;MQ=33.29;MQ0=14;MQRankSum=-8.822;QD=7.02;ReadPosRankSum=1.219 GT:AD:DP:GQ:PL 0/1:30,25:55:99:210,0,815 0/1:31,23:54:99:377,0,824 0/1:31,27:58:99:449,0,929 0/1:32,33:65:99:624,0,817 1 814215 . A G 910.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=3.515;DP=193;Dels=0.00;FS=122.458;HaplotypeScore=6.3193;MLEAC=4;MLEAF=0.500;MQ=35.78;MQ0=4;MQRankSum=-9.051;QD=4.72;ReadPosRankSum=2.254 GT:AD:DP:GQ:PL 0/1:29,21:51:99:341,0,698 0/1:31,12:43:99:106,0,807 0/1:35,14:49:99:160,0,949 0/1:28,21:50:99:336,0,796 1 814217 . C A 939.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.062;DP=187;Dels=0.00;FS=127.820;HaplotypeScore=6.1747;MLEAC=4;MLEAF=0.500;MQ=35.76;MQ0=4;MQRankSum=-9.203;QD=5.03;ReadPosRankSum=1.608 GT:AD:DP:GQ:PL 0/1:29,21:50:99:365,0,735 0/1:29,11:40:99:111,0,774 0/1:34,14:48:99:160,0,951 0/1:28,21:49:99:336,0,821 1 814244 . A G 638.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.422;DP=215;Dels=0.00;FS=45.921;HaplotypeScore=2.0851;MLEAC=4;MLEAF=0.500;MQ=37.14;MQ0=8;MQRankSum=-9.199;QD=2.97;ReadPosRankSum=-0.239 GT:AD:DP:GQ:PL 0/1:32,26:59:99:223,0,901 0/1:36,14:50:99:119,0,986 0/1:38,14:52:99:121,0,1119 0/1:34,20:54:99:208,0,990 1 814264 . C T 5446.35 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=-0.635;DP=219;Dels=0.00;FS=0.000;HaplotypeScore=1.0361;MLEAC=8;MLEAF=1.00;MQ=37.20;MQ0=6;MQRankSum=1.327;QD=24.87;ReadPosRankSum=0.037 GT:AD:DP:GQ:PL 1/1:1,62:63:99:1433,105,0 1/1:2,49:51:99:1313,120,0 1/1:1,52:53:99:1461,107,0 1/1:2,50:52:62:1265,62,0 1 814297 . T A 1244.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.254;DP=247;Dels=0.00;FS=1.216;HaplotypeScore=1.7513;MLEAC=4;MLEAF=0.500;MQ=37.39;MQ0=10;MQRankSum=-9.749;QD=5.04;ReadPosRankSum=2.894 GT:AD:DP:GQ:PL 0/1:33,44:77:99:489,0,866 0/1:36,29:65:99:456,0,1051 0/1:38,17:55:99:190,0,1136 0/1:31,19:50:99:142,0,884 1 814300 . T A 1214.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.910;DP=247;Dels=0.00;FS=0.576;HaplotypeScore=1.3075;MLEAC=4;MLEAF=0.500;MQ=37.42;MQ0=10;MQRankSum=-9.426;QD=4.92;ReadPosRankSum=3.426 GT:AD:DP:GQ:PL 0/1:32,44:76:99:486,0,843 0/1:38,28:66:99:460,0,1071 0/1:37,17:54:99:161,0,1099 0/1:33,18:51:99:140,0,876 1 814313 . C T 116.93 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=1.535;DP=240;Dels=0.00;FS=3.121;HaplotypeScore=0.4972;MLEAC=3;MLEAF=0.375;MQ=37.23;MQ0=11;MQRankSum=-4.871;QD=0.66;ReadPosRankSum=2.885 GT:AD:DP:GQ:PL 0/1:57,17:74:81:81,0,1195 0/0:57,6:63:65:0,65,1530 0/1:45,7:52:22:22,0,1163 0/1:43,8:51:48:48,0,988 1 814352 . A G 190.91 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=-1.063;DP=187;Dels=0.00;FS=0.954;HaplotypeScore=0.8123;MLEAC=2;MLEAF=0.250;MQ=33.27;MQ0=16;MQRankSum=-2.768;QD=1.87;ReadPosRankSum=0.817 GT:AD:DP:GQ:PL 0/1:36,10:46:99:111,0,709 0/1:45,10:55:99:114,0,1096 0/0:37,3:40:31:0,31,892 0/0:42,3:45:36:0,36,991 1 814392 . C T 2066.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=3.812;DP=222;Dels=0.00;FS=4.919;HaplotypeScore=5.3351;MLEAC=4;MLEAF=0.500;MQ=35.04;MQ0=20;MQRankSum=-2.078;QD=9.31;ReadPosRankSum=-3.407 GT:AD:DP:GQ:PL 0/1:24,23:47:99:565,0,498 0/1:28,39:67:99:689,0,765 0/1:18,30:48:99:433,0,489 0/1:32,22:54:99:412,0,710 1 814405 . T C 3292.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.019;DP=263;Dels=0.00;FS=6.194;HaplotypeScore=2.1716;MLEAC=4;MLEAF=0.500;MQ=38.70;MQ0=18;MQRankSum=-0.761;QD=12.52;ReadPosRankSum=-3.536 GT:AD:DP:GQ:PL 0/1:24,34:58:99:854,0,545 0/1:28,48:76:99:912,0,735 0/1:17,38:55:99:671,0,431 0/1:35,39:74:99:888,0,833 1 814459 . T C 5189.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.878;DP=357;Dels=0.00;FS=1.832;HaplotypeScore=2.0550;MLEAC=4;MLEAF=0.500;MQ=44.23;MQ0=9;MQRankSum=-6.992;QD=14.54;ReadPosRankSum=3.819 GT:AD:DP:GQ:PL 0/1:30,52:82:99:1369,0,709 0/1:33,62:95:99:1435,0,864 0/1:31,46:77:99:937,0,846 0/1:37,66:103:99:1481,0,810 1 814490 . C A 359.29 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-0.736;DP=284;Dels=0.00;FS=1.353;HaplotypeScore=11.2011;MLEAC=4;MLEAF=0.500;MQ=50.07;MQ0=3;MQRankSum=-4.066;QD=1.27;ReadPosRankSum=-1.909 GT:AD:DP:GQ:PL 0/1:58,9:67:93:93,0,1664 0/1:65,7:72:9:9,0,1863 0/1:54,7:61:22:22,0,1581 0/1:66,18:84:99:267,0,1710 1 814495 . C A 3120.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.219;DP=260;Dels=0.00;FS=9.866;HaplotypeScore=9.3962;MLEAC=4;MLEAF=0.500;MQ=50.14;MQ0=3;MQRankSum=-10.767;QD=12.00;ReadPosRankSum=-2.519 GT:AD:DP:GQ:PL 0/1:26,35:61:99:952,0,707 0/1:32,32:65:99:780,0,905 0/1:38,22:60:99:481,0,1123 0/1:31,43:74:99:940,0,806 1 814514 . G T 1182.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.734;DP=189;Dels=0.00;FS=15.144;HaplotypeScore=3.2085;MLEAC=4;MLEAF=0.500;MQ=52.69;MQ0=3;MQRankSum=-10.675;QD=6.26;ReadPosRankSum=-6.655 GT:AD:DP:GQ:PL 0/1:32,11:43:99:218,0,996 0/1:30,21:51:99:463,0,887 0/1:32,13:45:99:192,0,949 0/1:28,22:50:99:342,0,781 1 814518 . C T 490.98 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.990;DP=177;Dels=0.00;FS=3.278;HaplotypeScore=3.4582;MLEAC=4;MLEAF=0.500;MQ=53.81;MQ0=3;MQRankSum=-8.951;QD=2.77;ReadPosRankSum=-5.021 GT:AD:DP:GQ:PL 0/1:33,6:39:19:19,0,1037 0/1:31,16:47:99:307,0,850 0/1:33,7:41:48:48,0,1000 0/1:35,15:50:99:149,0,982 1 814524 . C T 220.07 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=3.162;DP=159;Dels=0.00;FS=0.000;HaplotypeScore=2.2664;MLEAC=3;MLEAF=0.375;MQ=55.80;MQ0=3;MQRankSum=-7.964;QD=1.83;ReadPosRankSum=-5.345 GT:AD:DP:GQ:PL 0/1:33,5:38:21:21,0,1034 0/1:30,11:41:99:197,0,881 0/0:35,4:39:4:0,4,1079 0/1:31,10:41:34:34,0,912 1 814525 . A G 103.34 PASS AC=1;AF=0.125;AN=8;BaseQRankSum=2.925;DP=151;Dels=0.00;FS=0.000;HaplotypeScore=1.7252;MLEAC=1;MLEAF=0.125;MQ=56.09;MQ0=3;MQRankSum=-7.042;QD=2.65;ReadPosRankSum=-4.294 GT:AD:DP:GQ:PL 0/0:32,3:35:38:0,38,1053 0/1:30,9:39:99:135,0,887 0/0:35,3:38:35:0,35,1119 0/0:31,8:39:37:0,37,985 1 814609 . A T 1061.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=0.866;DP=192;Dels=0.00;FS=44.428;HaplotypeScore=9.0075;MLEAC=4;MLEAF=0.500;MQ=52.25;MQ0=1;MQRankSum=-10.058;QD=5.53;ReadPosRankSum=2.067 GT:AD:DP:GQ:PL 0/1:20,18:38:99:435,0,522 0/1:36,22:58:99:386,0,1046 0/1:28,15:43:99:122,0,860 0/1:38,13:51:99:151,0,1093 1 814611 . A C 1273.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=3.920;DP=196;Dels=0.00;FS=40.953;HaplotypeScore=9.2575;MLEAC=4;MLEAF=0.500;MQ=52.13;MQ0=1;MQRankSum=-9.829;QD=6.50;ReadPosRankSum=1.718 GT:AD:DP:GQ:PL 0/1:21,20:41:99:491,0,545 0/1:36,24:60:99:471,0,1024 0/1:28,15:43:99:123,0,840 0/1:36,15:51:99:221,0,1050 1 814618 . A G 383.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.348;DP=206;Dels=0.00;FS=15.409;HaplotypeScore=11.2933;MLEAC=4;MLEAF=0.500;MQ=51.68;MQ0=1;MQRankSum=-5.248;QD=1.86;ReadPosRankSum=1.288 GT:AD:DP:GQ:PL 0/1:35,7:42:97:97,0,1023 0/1:56,11:67:99:171,0,1501 0/1:34,12:46:80:80,0,998 0/1:41,9:50:68:68,0,1212 1 814681 . A T 449.92 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-1.701;DP=229;Dels=0.00;FS=25.907;HaplotypeScore=0.7479;MLEAC=3;MLEAF=0.375;MQ=50.37;MQ0=0;MQRankSum=-4.418;QD=2.45;ReadPosRankSum=1.179 GT:AD:DP:GQ:PL 0/1:54,13:67:99:218,0,1521 0/1:46,15:61:99:222,0,1301 0/0:41,4:45:27:0,27,1261 0/1:48,7:55:44:44,0,1395 1 814694 . A C 1744.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-10.436;DP=206;Dels=0.00;FS=77.760;HaplotypeScore=1.6605;MLEAC=4;MLEAF=0.500;MQ=50.95;MQ0=0;MQRankSum=-9.955;QD=8.47;ReadPosRankSum=2.199 GT:AD:DP:GQ:PL 0/1:27,28:55:99:518,0,786 0/1:28,28:56:99:469,0,801 0/1:25,16:41:99:297,0,745 0/1:25,28:53:99:493,0,685 1 814710 . G A 1720.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-2.705;DP=198;Dels=0.00;FS=73.650;HaplotypeScore=4.9095;MLEAC=4;MLEAF=0.500;MQ=51.79;MQ0=0;MQRankSum=-10.785;QD=8.69;ReadPosRankSum=0.065 GT:AD:DP:GQ:PL 0/1:29,25:54:99:547,0,817 0/1:29,22:51:99:438,0,822 0/1:30,13:43:99:280,0,893 0/1:27,23:50:99:488,0,769 1 814731 . T C 988.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.515;DP=184;Dels=0.00;FS=70.581;HaplotypeScore=2.2664;MLEAC=4;MLEAF=0.500;MQ=53.63;MQ0=0;MQRankSum=-10.410;QD=5.37;ReadPosRankSum=-1.911 GT:AD:DP:GQ:PL 0/1:30,17:47:99:335,0,904 0/1:37,14:51:99:283,0,1094 0/1:34,9:43:99:144,0,992 0/1:28,15:43:99:259,0,821 1 814742 . C G 481.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.033;DP=167;Dels=0.00;FS=65.314;HaplotypeScore=1.5026;MLEAC=4;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-9.179;QD=2.89;ReadPosRankSum=-2.773 GT:AD:DP:GQ:PL 0/1:33,12:45:99:197,0,984 0/1:34,9:43:99:138,0,998 0/1:35,8:43:99:108,0,1035 0/1:29,7:36:71:71,0,811 1 815181 . G T 39.91 LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-1.760;DP=186;Dels=0.00;FS=30.376;HaplotypeScore=3.5218;MLEAC=2;MLEAF=0.250;MQ=54.09;MQ0=5;MQRankSum=-8.136;QD=0.36;ReadPosRankSum=2.016 GT:AD:DP:GQ:PL 0/0:22,2:24:63:0,63,743 0/1:46,14:60:45:45,0,1368 0/1:41,11:52:29:29,0,1215 0/0:45,5:50:38:0,38,1368 1 815197 . T C 41.91 LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-5.342;DP=179;Dels=0.00;FS=29.810;HaplotypeScore=1.3510;MLEAC=2;MLEAF=0.250;MQ=53.95;MQ0=5;MQRankSum=-8.111;QD=0.39;ReadPosRankSum=5.186 GT:AD:DP:GQ:PL 0/0:23,2:25:63:0,63,739 0/1:45,12:57:45:45,0,1348 0/1:40,10:50:31:31,0,1224 0/0:42,5:47:36:0,36,1265 1 815277 . T C 56.53 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.034;DP=170;Dels=0.00;FS=12.024;HaplotypeScore=5.0587;MLEAC=3;MLEAF=0.375;MQ=49.33;MQ0=8;MQRankSum=-5.425;QD=0.41;ReadPosRankSum=-2.683 GT:AD:DP:GQ:PL 0/0:30,3:33:11:0,11,805 0/1:39,8:47:41:41,0,1114 0/1:39,7:46:33:33,0,1123 0/1:38,6:44:16:16,0,1065 1 815337 . G T 295.96 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-1.037;DP=185;Dels=0.00;FS=20.230;HaplotypeScore=4.3260;MLEAC=4;MLEAF=0.500;MQ=43.12;MQ0=16;MQRankSum=-5.716;QD=1.60;ReadPosRankSum=0.588 GT:AD:DP:GQ:PL 0/1:30,8:38:24:24,0,748 0/1:38,12:50:87:87,0,993 0/1:32,10:42:99:123,0,886 0/1:45,9:54:94:94,0,1216 1 815373 . C T 41.52 LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-1.125;DP=156;Dels=0.00;FS=33.434;HaplotypeScore=2.1193;MLEAC=2;MLEAF=0.250;MQ=48.98;MQ0=14;MQRankSum=-7.522;QD=0.50;ReadPosRankSum=-1.252 GT:AD:DP:GQ:PL 0/1:29,9:39:6:6,0,836 0/0:27,15:42:55:0,55,877 0/0:24,7:31:20:0,20,787 0/1:36,7:43:68:68,0,1079 1 815463 . T C 715.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.145;DP=203;Dels=0.00;FS=8.878;HaplotypeScore=9.1764;MLEAC=4;MLEAF=0.500;MQ=44.29;MQ0=11;MQRankSum=-10.931;QD=3.53;ReadPosRankSum=-2.334 GT:AD:DP:GQ:PL 0/1:23,12:35:79:79,0,686 0/1:38,25:63:99:279,0,1006 0/1:35,21:56:99:173,0,990 0/1:28,21:49:99:217,0,768 1 815469 . G T 194.10 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=1.114;DP=223;Dels=0.00;FS=9.672;HaplotypeScore=11.8201;MLEAC=2;MLEAF=0.250;MQ=44.38;MQ0=10;MQRankSum=-5.697;QD=1.55;ReadPosRankSum=-1.250 GT:AD:DP:GQ:PL 0/0:34,4:38:55:0,55,967 0/1:56,11:67:71:71,0,1316 0/0:51,9:60:5:0,5,1194 0/1:45,13:58:99:156,0,1095 1 815497 . A G 1945.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=2.694;DP=282;Dels=0.00;FS=33.913;HaplotypeScore=5.1705;MLEAC=4;MLEAF=0.500;MQ=43.86;MQ0=6;MQRankSum=-10.870;QD=6.90;ReadPosRankSum=2.613 GT:AD:DP:GQ:PL 0/1:29,21:50:99:351,0,731 0/1:46,39:86:99:563,0,1221 0/1:35,33:68:99:437,0,951 0/1:40,37:77:99:627,0,1002 1 815520 . C T 3095.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.941;DP=305;Dels=0.00;FS=4.101;HaplotypeScore=12.2350;MLEAC=4;MLEAF=0.500;MQ=43.53;MQ0=7;MQRankSum=-13.985;QD=10.15;ReadPosRankSum=1.418 GT:AD:DP:GQ:PL 0/1:23,35:58:99:539,0,599 0/1:26,56:82:99:909,0,698 0/1:33,39:72:99:613,0,983 0/1:30,61:91:99:1067,0,783 1 815573 . C T 1621.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.819;DP=249;Dels=0.00;FS=4.524;HaplotypeScore=5.3895;MLEAC=4;MLEAF=0.500;MQ=46.21;MQ0=15;MQRankSum=-13.173;QD=6.51;ReadPosRankSum=1.228 GT:AD:DP:GQ:PL 0/1:25,26:51:99:346,0,706 0/1:30,37:67:99:469,0,860 0/1:24,27:52:99:336,0,674 0/1:40,39:79:99:503,0,1180 1 815601 . T C 405.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.013;DP=187;Dels=0.01;FS=10.669;HaplotypeScore=5.9834;MLEAC=4;MLEAF=0.500;MQ=49.19;MQ0=15;MQRankSum=-9.435;QD=2.17;ReadPosRankSum=-4.126 GT:AD:DP:GQ:PL 0/1:22,12:34:91:91,0,615 0/1:38,19:57:99:120,0,1135 0/1:30,12:42:92:92,0,880 0/1:34,18:52:99:135,0,942 1 815611 . C T 124.99 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=4.360;DP=156;Dels=0.00;FS=0.000;HaplotypeScore=6.6208;MLEAC=2;MLEAF=0.250;MQ=50.85;MQ0=15;MQRankSum=-8.557;QD=1.58;ReadPosRankSum=-4.134 GT:AD:DP:GQ:PL 0/1:19,10:29:34:34,0,515 0/1:32,18:50:99:125,0,849 0/0:27,9:36:17:0,17,729 0/0:30,11:41:37:0,37,829 1 815662 . G T 3559.35 PASS AC=8;AF=1.00;AN=8;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=0.3281;MLEAC=8;MLEAF=1.00;MQ=59.72;MQ0=1;QD=33.26 GT:AD:DP:GQ:PL 1/1:1,23:24:69:823,69,0 1/1:0,31:31:90:993,90,0 1/1:0,31:31:90:1060,90,0 1/1:0,21:21:63:709,63,0 1 815681 . G T 3060.36 PASS AC=8;AF=1.00;AN=8;BaseQRankSum=0.577;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=1.1047;MLEAC=8;MLEAF=1.00;MQ=59.39;MQ0=1;MQRankSum=-1.155;QD=31.23;ReadPosRankSum=-0.541 GT:AD:DP:GQ:PL 1/1:2,20:22:31:649,31,0 1/1:0,28:28:81:886,81,0 1/1:0,33:33:96:1090,96,0 1/1:0,14:14:42:461,42,0 1 815728 . A G 660.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-3.681;DP=166;Dels=0.00;FS=76.748;HaplotypeScore=6.2820;MLEAC=4;MLEAF=0.500;MQ=53.33;MQ0=3;MQRankSum=-9.553;QD=3.98;ReadPosRankSum=6.864 GT:AD:DP:GQ:PL 0/1:29,8:37:99:132,0,775 0/1:33,15:48:99:221,0,939 0/1:33,9:42:99:116,0,988 0/1:23,15:38:99:224,0,669 1 815757 . G A 905.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=3.561;DP=194;Dels=0.00;FS=89.480;HaplotypeScore=2.1639;MLEAC=4;MLEAF=0.500;MQ=51.26;MQ0=4;MQRankSum=-10.882;QD=4.67;ReadPosRankSum=-2.373 GT:AD:DP:GQ:PL 0/1:32,13:45:99:228,0,915 0/1:31,21:52:99:317,0,879 0/1:39,10:49:62:62,0,1222 0/1:26,22:48:99:331,0,727 1 815803 . G A 960.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=5.743;DP=185;Dels=0.00;FS=64.905;HaplotypeScore=1.3209;MLEAC=4;MLEAF=0.500;MQ=50.31;MQ0=6;MQRankSum=-11.056;QD=5.19;ReadPosRankSum=3.500 GT:AD:DP:GQ:PL 0/1:28,12:41:99:152,0,828 0/1:27,20:47:99:339,0,754 0/1:34,12:46:99:107,0,1029 0/1:25,26:51:99:395,0,703 1 815804 . T G 898.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.320;DP=188;Dels=0.00;FS=64.867;HaplotypeScore=1.3209;MLEAC=4;MLEAF=0.500;MQ=50.19;MQ0=6;MQRankSum=-11.126;QD=4.78;ReadPosRankSum=3.697 GT:AD:DP:GQ:PL 0/1:30,12:42:99:142,0,845 0/1:27,20:47:99:315,0,773 0/1:35,13:48:99:102,0,962 0/1:25,26:51:99:372,0,698 1 815815 . A T 948.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-2.028;DP=202;Dels=0.00;FS=67.118;HaplotypeScore=2.5257;MLEAC=4;MLEAF=0.500;MQ=48.60;MQ0=8;MQRankSum=-11.720;QD=4.70;ReadPosRankSum=3.304 GT:AD:DP:GQ:PL 0/1:29,16:45:99:188,0,841 0/1:25,23:48:99:324,0,734 0/1:35,16:51:99:101,0,1049 0/1:28,30:58:99:368,0,823 1 815853 . A G 287.95 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-6.535;DP=148;Dels=0.00;FS=58.139;HaplotypeScore=0.7231;MLEAC=4;MLEAF=0.500;MQ=50.15;MQ0=5;MQRankSum=-9.376;QD=1.95;ReadPosRankSum=3.628 GT:AD:DP:GQ:PL 0/1:21,7:28:31:31,0,626 0/1:21,11:32:85:85,0,654 0/1:30,14:44:74:74,0,940 0/1:29,15:44:99:130,0,882 1 815857 . C T 254.95 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-2.273;DP=141;Dels=0.00;FS=57.911;HaplotypeScore=0.4864;MLEAC=4;MLEAF=0.500;MQ=50.04;MQ0=4;MQRankSum=-9.075;QD=1.81;ReadPosRankSum=3.790 GT:AD:DP:GQ:PL 0/1:21,7:28:29:29,0,645 0/1:21,9:30:58:58,0,637 0/1:28,14:42:92:92,0,860 0/1:28,13:41:99:108,0,815 1 815873 . G T 61.32 LowQD AC=3;AF=0.375;AN=8;BaseQRankSum=-2.332;DP=140;Dels=0.00;FS=42.926;HaplotypeScore=2.2135;MLEAC=3;MLEAF=0.375;MQ=49.26;MQ0=3;MQRankSum=-8.341;QD=0.55;ReadPosRankSum=0.226 GT:AD:DP:GQ:PL 0/0:23,5:28:4:0,4,681 0/1:20,8:28:34:34,0,615 0/1:31,13:44:54:54,0,931 0/1:31,9:40:4:4,0,941 1 816636 . G A 72.90 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=4.261;DP=159;Dels=0.00;FS=29.630;HaplotypeScore=2.6390;MLEAC=2;MLEAF=0.250;MQ=49.00;MQ0=12;MQRankSum=-6.916;QD=0.95;ReadPosRankSum=0.730 GT:AD:DP:GQ:PL 0/1:24,6:32:58:58,0,464 0/0:36,6:42:61:0,61,854 0/0:33,7:40:35:0,35,879 0/1:29,16:45:49:49,0,657 1 816638 . T C 68.91 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=1.456;DP=156;Dels=0.00;FS=28.839;HaplotypeScore=2.3893;MLEAC=2;MLEAF=0.250;MQ=48.77;MQ0=12;MQRankSum=-6.953;QD=0.91;ReadPosRankSum=0.906 GT:AD:DP:GQ:PL 0/1:26,6:32:50:50,0,559 0/0:36,5:41:59:0,59,896 0/0:32,7:39:29:0,29,935 0/1:28,16:44:53:53,0,721 1 816642 . T C 65.90 LowQD AC=2;AF=0.250;AN=8;BaseQRankSum=-4.495;DP=156;Dels=0.00;FS=28.269;HaplotypeScore=2.4256;MLEAC=2;MLEAF=0.250;MQ=48.50;MQ0=13;MQRankSum=-6.830;QD=0.88;ReadPosRankSum=1.656 GT:AD:DP:GQ:PL 0/1:25,6:31:49:49,0,645 0/0:33,6:39:50:0,50,812 0/0:35,7:42:38:0,38,1040 0/1:28,16:44:51:51,0,723 1 816680 . G T 188.57 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=7.670;DP=159;Dels=0.00;FS=14.659;HaplotypeScore=14.9001;MLEAC=3;MLEAF=0.375;MQ=44.95;MQ0=15;MQRankSum=-9.145;QD=1.19;ReadPosRankSum=-0.682 GT:AD:DP:GQ:PL 0/1:13,9:26:53:53,0,329 0/1:27,18:49:61:61,0,656 0/1:24,14:43:99:143,0,664 0/1:17,15:41:12:12,0,417 1 816682 . G A 527.94 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-0.110;DP=171;Dels=0.00;FS=35.421;HaplotypeScore=16.8926;MLEAC=4;MLEAF=0.500;MQ=44.47;MQ0=14;MQRankSum=-9.751;QD=3.09;ReadPosRankSum=0.034 GT:AD:DP:GQ:PL 0/1:15,12:27:99:143,0,411 0/1:29,20:49:68:68,0,865 0/1:29,15:45:99:124,0,825 0/1:21,29:50:99:225,0,569 1 816689 . T C 32.05 LowQD;LowQual AC=2;AF=0.250;AN=8;BaseQRankSum=-2.735;DP=212;Dels=0.00;FS=6.264;HaplotypeScore=30.9612;MLEAC=2;MLEAF=0.250;MQ=43.36;MQ0=14;MQRankSum=-2.554;QD=0.26;ReadPosRankSum=-0.661 GT:AD:DP:GQ:PL 0/0:35,2:37:55:0,55,936 0/1:53,7:60:18:18,0,1140 0/0:46,5:51:23:0,23,1209 0/1:57,7:64:48:48,0,1144 1 816696 . G T 206.20 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.290;DP=232;Dels=0.00;FS=0.923;HaplotypeScore=16.5729;MLEAC=4;MLEAF=0.500;MQ=42.94;MQ0=17;MQRankSum=-5.087;QD=0.89;ReadPosRankSum=-1.664 GT:AD:DP:GQ:PL 0/1:32,10:43:99:128,0,700 0/1:52,14:66:10:10,0,1275 0/1:50,6:56:4:4,0,1182 0/1:52,15:67:95:95,0,1103 1 816697 . A T 268.95 LowQD AC=4;AF=0.500;AN=8;BaseQRankSum=-1.338;DP=232;Dels=0.00;FS=23.133;HaplotypeScore=16.5729;MLEAC=4;MLEAF=0.500;MQ=42.76;MQ0=18;MQRankSum=-4.068;QD=1.16;ReadPosRankSum=-0.146 GT:AD:DP:GQ:PL 0/1:37,6:43:34:34,0,821 0/1:58,8:66:58:58,0,1221 0/1:45,11:56:92:92,0,1052 0/1:54,13:67:99:117,0,1075 bio-vcf-0.9.5/test/data/input/multisample.vcf000066400000000000000000000616101400124230400211270ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550 1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296 GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344 1 10665 . C G 56.61 . AC=2;AF=0.250;AN=8;BaseQRankSum=2.219;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=25.41;MQ0=15;MQRankSum=0.185;QD=4.72;ReadPosRankSum=1.849 GT:AD:DP:GQ:PL ./. ./. 0/1:4,3:7:57:57,0,78 0/1:3,2:5:23:30,0,23 ./. 0/0:2,0:2:3:0,3,26 0/0:6,1:7:6:0,6,49 1 10694 . C G 85.78 . AC=4;AF=1.00;AN=4;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=17.21;MQ0=17;QD=8.58 GT:AD:DP:GQ:PL ./. ./. 1/1:2,3:5:6:74,6,0 1/1:3,2:5:3:35,3,0 ./. ./. ./. 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL ./. ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33 1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417 1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128 1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079 1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596 1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921 1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230 1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767 1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677 1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178 GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86 1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310 1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620 1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326 1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003 1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055 1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934 1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861 1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246 1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193 1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827 1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895 1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285 1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472 1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706 1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760 1 16103 . T G 2348.85 . 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GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:23:11,12,0,0:0,0,23,0:96:36:0:59:37:37:0:. 0/1:0/1:6:1,3,1,1:2,0,4,0:29:36:29:60,60:37:37,37:2:36 4 82058553 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:37:0:60:37:37:0:. 0/1:0/1:4:2,0,2,0:0,2,0,2:30:37:30:60,60:37:37,37:2:30 4 122769998 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:7,0,0,0:0,7,0,0:48:40:0:54:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:30 5 13850856 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:3,5,0,0:0,0,8,0:51:40:0:51:37:37:0:. 0/1:0/1:3:0,1,2,0:0,2,1,0:1:40:33:49,60:37:37,37:2:33 5 132038609 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:10,2,0,0:0,12,0,0:63:33:0:58:37:37:0:. 0/1:0/1:7:3,2,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:33 5 137756599 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:7,6,0,0:0,13,0,0:66:31:0:60:37:37:0:. 0/1:0/1:6:2,2,2,0:0,4,0,2:24:31:24:60,60:37:37,37:2:31 5 141974902 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:9,5,0,0:0,14,0,0:69:40:0:60:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:40 6 2749400 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,10,0,0:57:35:0:60:37:37:0:. 0/1:0/1:4:2,0,0,2:0,2,0,2:28:35:28:60,39:37:37,37:2:34 7 95217113 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:36:0:60:37:37:0:. 0/1:0/1:6:1,3,1,1:2,0,4,0:29:36:29:60,60:37:37,37:2:30 7 140434525 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:8,6,0,0:0,0,14,0:69:31:0:59:37:37:0:. 0/1:0/1:6:3,1,0,2:2,0,4,0:24:31:24:60,58:37:37,37:2:31 7 151856059 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:20:9,10,1,0:0,19,0,1:50:33:0:59:37:37:0:. 0/1:0/1:7:1,4,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:30 8 42958817 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:6,6,0,0:0,12,0,0:60:36:0:55:37:37:0:. 0/1:0/1:7:4,1,1,1:0,5,0,2:29:36:29:48,60:37:37,37:2:35 8 131070237 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:9,4,0,0:13,0,0,0:66:39:0:60:37:37:0:. 0/1:0/1:5:2,1,1,1:3,0,2,0:32:39:32:60,60:37:37,37:2:39 8 141711010 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,10,0,0:57:40:0:59:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,55:37:37,37:2:37 8 145059674 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:7,7,0,0:0,14,0,0:69:34:0:56:37:37:0:. 0/1:0/1:5:2,1,0,2:0,3,0,2:27:34:27:60,60:37:37,37:2:34 9 111651620 . A T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:4,3,0,0:7,0,0,0:48:92:0:60:37:37:0:. 0/1:0/1:7:1,2,3,1:3,0,0,4:58:92:85:60,60:37:37,37:2:31 9 111685156 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:9,4,0,0:0,0,13,0:66:37:0:60:37:37:0:. 0/1:0/1:4:1,1,2,0:2,0,2,0:12:37:30:60,37:37:37,37:2:37 10 6525571 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:0,8,0,0:0,0,8,0:51:37:0:55:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:32 10 97197246 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:7,3,0,0:0,10,0,0:57:39:0:58:37:37:0:. 0/1:0/1:5:3,0,1,1:0,3,0,2:32:39:32:60,53:37:37,37:2:36 11 58949455 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:8,4,0,0:0,0,12,0:60:33:0:54:37:37:0:. 0/1:0/1:7:3,2,1,1:2,0,5,0:26:33:26:60,36:37:37,37:2:33 11 65481082 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:17:12,5,0,0:0,0,17,0:78:45:0:58:37:37:0:. 0/1:0/1:3:0,1,1,1:2,0,1,0:1:45:34:60,60:37:37,37:2:45 11 94180424 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:23:17,6,0,0:0,0,23,0:96:34:0:56:37:37:0:. 0/1:0/1:5:2,1,2,0:2,0,3,0:27:34:27:60,59:37:37,37:2:34 11 121036021 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:3,9,0,0:0,12,0,0:63:31:0:59:37:37:0:. 0/1:0/1:6:4,0,0,2:0,4,0,2:24:31:24:59,60:37:37,37:2:31 12 994952 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:1,8,0,0:0,9,0,0:54:33:0:59:37:37:0:. 0/1:0/1:7:2,3,1,1:0,5,0,2:26:33:26:51,55:37:37,37:2:32 12 69233187 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:5,4,0,0:0,9,0,0:51:33:0:53:37:37:0:. 0/1:0/1:7:4,1,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:30 12 77436879 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:4,6,0,0:0,0,10,0:57:34:0:60:37:37:0:. 0/1:0/1:5:2,1,0,2:2,0,3,0:27:34:27:60,60:37:37,37:2:33 12 96641273 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:4,4,0,0:0,0,8,0:51:33:0:60:37:37:0:. 0/1:0/1:7:2,3,1,1:2,0,5,0:26:33:26:60,50:37:37,37:2:30 12 110813986 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:4,4,0,0:0,0,8,0:51:39:0:59:37:37:0:. 0/1:0/1:5:1,2,1,1:2,0,3,0:32:39:32:60,60:37:37,37:2:33 12 122825587 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:21:12,9,0,0:0,21,0,0:90:34:0:59:37:37:0:. 0/1:0/1:5:3,0,2,0:0,3,0,2:27:34:27:60,60:37:37,37:2:34 14 30135337 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,7,0,0:48:40:0:60:37:37:0:. 0/1:0/1:3:1,0,0,2:0,1,0,2:1:40:33:60,60:37:37,37:2:30 14 51398458 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:4,5,0,0:0,0,9,0:54:36:0:55:37:37:0:. 0/1:0/1:6:0,4,1,1:2,0,4,0:29:36:29:60,59:37:37,37:2:33 15 43170722 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:31:0:60:37:37:0:. 0/1:0/1:6:4,0,2,0:0,4,0,2:24:31:24:56,54:37:37,37:2:31 15 50862183 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:7,2,0,0:0,9,0,0:54:35:0:60:37:37:0:. 0/1:0/1:4:0,2,0,2:2,2,0,0:28:35:28:45,59:37:37,37:2:33 15 64332347 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:39:0:60:37:37:0:. 0/1:0/1:5:3,0,1,1:0,3,0,2:32:39:32:58,56:37:37,37:2:30 15 80845030 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:1,8,0,0:0,9,0,0:54:31:0:60:37:37:0:. 0/1:0/1:6:2,2,2,0:0,4,0,2:24:31:24:60,60:37:37,37:2:30 16 1812938 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:8,3,0,0:0,0,11,0:60:34:0:46:37:37:0:. 0/1:0/1:5:1,2,1,1:2,0,3,0:27:34:27:46,55:37:37,37:2:33 16 3582808 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:6,4,0,0:0,0,10,0:57:34:0:59:37:37:0:. 0/1:0/1:5:0,3,2,0:2,0,3,0:27:34:27:60,60:37:37,37:2:33 16 14042032 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:37:0:60:37:37:0:. 0/1:0/1:4:0,2,2,0:0,2,0,2:30:37:30:57,60:37:37,37:2:30 16 23619204 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:42:0:60:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,60:37:37,37:2:31 17 41256142 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:5,3,0,0:0,0,8,0:51:40:0:60:37:37:0:. 0/1:0/1:3:0,1,2,0:2,0,1,0:1:40:33:57,60:37:37,37:2:33 17 61784013 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,9,0,0:54:45:0:60:37:37:0:. 0/1:0/1:3:0,1,1,1:0,1,0,2:1:45:34:60,60:37:37,37:2:36 18 45423074 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:16:8,8,0,0:0,16,0,0:75:46:0:53:37:37:0:. 0/1:0/1:10:3,4,3,0:0,7,0,3:39:46:39:60,60:37:37,37:2:46 18 60985432 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:9,4,0,1:0,0,13,0:32:42:0:60:37:37:0:. 0/1:0/1:4:2,0,1,1:2,0,2,0:30:42:35:60,57:37:37,37:2:41 19 39664512 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:8,6,0,0:0,14,0,0:69:42:0:60:37:37:0:. 0/1:0/1:4:0,2,1,1:0,2,0,2:30:42:35:60,60:37:37,37:2:42 19 49473085 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:4,4,0,0:0,0,8,0:51:37:0:60:37:37:0:. 0/1:0/1:4:1,1,2,0:0,2,2,0:30:37:30:48,56:37:37,37:2:32 20 34135210 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:2,6,0,0:0,8,0,0:51:36:0:59:37:37:0:. 0/1:0/1:6:2,2,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:32 20 35663882 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:2,5,0,0:0,0,7,0:48:37:0:56:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:30 X 70341572 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:33:0:56:37:37:0:. 0/1:0/1:7:3,2,1,1:0,5,0,2:26:33:26:58,60:37:37,37:2:33 X 123164862 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:40:0:59:37:37:0:. 0/1:0/1:3:1,0,2,0:2,0,1,0:1:40:33:60,60:37:37,37:2:30 bio-vcf-0.9.5/test/data/regression/000077500000000000000000000000001400124230400171105ustar00rootroot00000000000000bio-vcf-0.9.5/test/data/regression/empty.ref000066400000000000000000000000741400124230400207450ustar00rootroot00000000000000##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO bio-vcf-0.9.5/test/data/regression/eval_once.ref000066400000000000000000000100251400124230400215370ustar00rootroot00000000000000{"UnifiedGenotyper"=>{"ID"=>"UnifiedGenotyper", "Version"=>"2.8-1-g932cd3a", "Date"=>"Sat Jan 25 10:33:56 CET 2014", "Epoch"=>1390642436187, "CommandLineOptions"=>"analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"}} bio-vcf-0.9.5/test/data/regression/eval_r.info.dp.ref000066400000000000000000000264071400124230400224230ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= 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GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:4,5,0,0:0,0,9,0:54:36:0:55:37:37:0:. 0/1:0/1:6:0,4,1,1:2,0,4,0:29:36:29:60,59:37:37,37:2:33 15 43170722 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:31:0:60:37:37:0:. 0/1:0/1:6:4,0,2,0:0,4,0,2:24:31:24:56,54:37:37,37:2:31 15 50862183 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:7,2,0,0:0,9,0,0:54:35:0:60:37:37:0:. 0/1:0/1:4:0,2,0,2:2,2,0,0:28:35:28:45,59:37:37,37:2:33 15 64332347 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:39:0:60:37:37:0:. 0/1:0/1:5:3,0,1,1:0,3,0,2:32:39:32:58,56:37:37,37:2:30 15 80845030 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:1,8,0,0:0,9,0,0:54:31:0:60:37:37:0:. 0/1:0/1:6:2,2,2,0:0,4,0,2:24:31:24:60,60:37:37,37:2:30 16 1812938 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:8,3,0,0:0,0,11,0:60:34:0:46:37:37:0:. 0/1:0/1:5:1,2,1,1:2,0,3,0:27:34:27:46,55:37:37,37:2:33 16 3582808 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:6,4,0,0:0,0,10,0:57:34:0:59:37:37:0:. 0/1:0/1:5:0,3,2,0:2,0,3,0:27:34:27:60,60:37:37,37:2:33 16 14042032 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:37:0:60:37:37:0:. 0/1:0/1:4:0,2,2,0:0,2,0,2:30:37:30:57,60:37:37,37:2:30 16 23619204 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:42:0:60:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,60:37:37,37:2:31 17 41256142 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:5,3,0,0:0,0,8,0:51:40:0:60:37:37:0:. 0/1:0/1:3:0,1,2,0:2,0,1,0:1:40:33:57,60:37:37,37:2:33 17 61784013 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,9,0,0:54:45:0:60:37:37:0:. 0/1:0/1:3:0,1,1,1:0,1,0,2:1:45:34:60,60:37:37,37:2:36 18 45423074 . C T . PASS . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:16:8,8,0,0:0,16,0,0:75:46:0:53:37:37:0:. 0/1:0/1:10:3,4,3,0:0,7,0,3:39:46:39:60,60:37:37,37:2:46 18 60985432 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:9,4,0,1:0,0,13,0:32:42:0:60:37:37:0:. 0/1:0/1:4:2,0,1,1:2,0,2,0:30:42:35:60,57:37:37,37:2:41 19 39664512 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:8,6,0,0:0,14,0,0:69:42:0:60:37:37:0:. 0/1:0/1:4:0,2,1,1:0,2,0,2:30:42:35:60,60:37:37,37:2:42 19 49473085 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:4,4,0,0:0,0,8,0:51:37:0:60:37:37:0:. 0/1:0/1:4:1,1,2,0:0,2,2,0:30:37:30:48,56:37:37,37:2:32 20 34135210 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:2,6,0,0:0,8,0,0:51:36:0:59:37:37:0:. 0/1:0/1:6:2,2,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:32 20 35663882 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:2,5,0,0:0,0,7,0:48:37:0:56:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:30 X 70341572 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:33:0:56:37:37:0:. 0/1:0/1:7:3,2,1,1:0,5,0,2:26:33:26:58,60:37:37,37:2:33 X 123164862 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:40:0:59:37:37:0:. 0/1:0/1:3:1,0,2,0:2,0,1,0:1:40:33:60,60:37:37,37:2:30 bio-vcf-0.9.5/test/data/regression/r.info.dp.ref000066400000000000000000000602021400124230400214030ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550 1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296 GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344 1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417 1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128 1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079 1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596 1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921 1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230 1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767 1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677 1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178 GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86 1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310 1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620 1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326 1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003 1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055 1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934 1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861 1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246 1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193 1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827 1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895 1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285 1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472 1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706 1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760 1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641 bio-vcf-0.9.5/test/data/regression/rewrite.info.sample.ref000066400000000000000000000625341400124230400235130ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551;sample=XXXXX GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640;sample=XXXXX GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927;sample=XXXXX GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756;sample=XXXXX GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373;sample=XXXXX GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815;sample=XXXXX GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957;sample=XXXXX GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550 1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296;sample=XXXXX GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344 1 10665 . C G 56.61 . AC=2;AF=0.250;AN=8;BaseQRankSum=2.219;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=25.41;MQ0=15;MQRankSum=0.185;QD=4.72;ReadPosRankSum=1.849;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 0/1:4,3:7:57:57,0,78 0/1:3,2:5:23:30,0,23 ./. 0/0:2,0:2:3:0,3,26 0/0:6,1:7:6:0,6,49 1 10694 . C G 85.78 . AC=4;AF=1.00;AN=4;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=17.21;MQ0=17;QD=8.58;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 1/1:2,3:5:6:74,6,0 1/1:3,2:5:3:35,3,0 ./. ./. ./. 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33 1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195;sample=XXXXX GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417 1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079;sample=XXXXX GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128 1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437;sample=XXXXX GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079 1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383;sample=XXXXX GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596 1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193;sample=XXXXX GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921 1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309;sample=XXXXX GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230 1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283;sample=XXXXX GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767 1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433;sample=XXXXX GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677 1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178;sample=XXXXX GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86 1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294;sample=XXXXX GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310 1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039;sample=XXXXX GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620 1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696;sample=XXXXX GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326 1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653;sample=XXXXX GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003 1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785;sample=XXXXX GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055 1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752;sample=XXXXX GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934 1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181;sample=XXXXX GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861 1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560;sample=XXXXX GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246 1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291;sample=XXXXX GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193 1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530;sample=XXXXX GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827 1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972;sample=XXXXX GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895 1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707;sample=XXXXX GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285 1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088;sample=XXXXX GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472 1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355;sample=XXXXX GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706 1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448;sample=XXXXX GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760 1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044;sample=XXXXX GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641 bio-vcf-0.9.5/test/data/regression/s.dp.ref000066400000000000000000000566401400124230400204650ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550 1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417 1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128 1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079 1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596 1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921 1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230 1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767 1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677 1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310 1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620 1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326 1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003 1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055 1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934 1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861 1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246 1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193 1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827 1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895 1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285 1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472 1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706 1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760 1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641 bio-vcf-0.9.5/test/data/regression/seval_s.dp.ref000066400000000000000000000022321400124230400216430ustar00rootroot000000000000001 10257 159 242 249 249 186 212 218 1 10291 165 249 249 247 161 163 189 1 10297 182 246 250 246 165 158 183 1 10303 198 247 248 248 172 157 182 1 10315 212 246 242 245 190 157 189 1 10321 218 246 248 248 193 164 196 1 10327 237 238 229 237 209 183 210 1 10583 8 24 21 23 15 19 19 1 10665 7 5 2 7 1 10694 5 5 1 10723 4 5 6 1 12783 58 164 144 182 126 103 158 1 13116 32 131 102 152 104 88 109 1 13118 34 129 101 145 99 85 108 1 13178 52 172 137 172 129 119 148 1 13302 36 136 99 146 90 65 117 1 13757 53 201 181 250 152 130 182 1 13868 75 192 182 224 142 111 167 1 13896 62 135 143 175 112 81 121 1 14354 43 158 115 145 72 119 1 14464 51 155 141 150 83 89 140 1 14673 36 142 117 157 95 76 131 1 14699 43 128 109 147 98 78 114 1 14907 57 216 162 205 153 118 158 1 14930 68 216 170 210 136 125 164 1 14933 68 216 169 212 132 128 164 1 14948 63 192 181 211 129 121 153 1 14976 56 166 161 196 109 116 135 1 15118 46 198 129 230 113 126 158 1 15190 53 208 170 200 126 145 179 1 15211 54 183 161 171 120 134 168 1 15274 37 121 102 137 71 67 98 1 15447 46 242 183 226 137 173 175 1 15688 37 182 147 184 100 101 148 1 16068 33 57 68 81 49 49 58 1 16103 50 79 86 106 60 61 84 bio-vcf-0.9.5/test/data/regression/sfilter_seval_s.dp.ref000066400000000000000000000020511400124230400233720ustar00rootroot000000000000001 10257 159 242 249 249 186 212 218 1 10291 165 249 249 247 161 163 189 1 10297 182 246 250 246 165 158 183 1 10303 198 247 248 248 172 157 182 1 10315 212 246 242 245 190 157 189 1 10321 218 246 248 248 193 164 196 1 10327 237 238 229 237 209 183 210 1 12783 58 164 144 182 126 103 158 1 13116 32 131 102 152 104 88 109 1 13118 34 129 101 145 99 85 108 1 13178 52 172 137 172 129 119 148 1 13302 36 136 99 146 90 65 117 1 13757 53 201 181 250 152 130 182 1 13868 75 192 182 224 142 111 167 1 13896 62 135 143 175 112 81 121 1 14464 51 155 141 150 83 89 140 1 14673 36 142 117 157 95 76 131 1 14699 43 128 109 147 98 78 114 1 14907 57 216 162 205 153 118 158 1 14930 68 216 170 210 136 125 164 1 14933 68 216 169 212 132 128 164 1 14948 63 192 181 211 129 121 153 1 14976 56 166 161 196 109 116 135 1 15118 46 198 129 230 113 126 158 1 15190 53 208 170 200 126 145 179 1 15211 54 183 161 171 120 134 168 1 15274 37 121 102 137 71 67 98 1 15447 46 242 183 226 137 173 175 1 15688 37 182 147 184 100 101 148 1 16068 33 57 68 81 49 49 58 1 16103 50 79 86 106 60 61 84 bio-vcf-0.9.5/test/data/regression/thread4.ref000066400000000000000000000616101400124230400211450ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550 1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296 GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344 1 10665 . C G 56.61 . AC=2;AF=0.250;AN=8;BaseQRankSum=2.219;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=25.41;MQ0=15;MQRankSum=0.185;QD=4.72;ReadPosRankSum=1.849 GT:AD:DP:GQ:PL ./. ./. 0/1:4,3:7:57:57,0,78 0/1:3,2:5:23:30,0,23 ./. 0/0:2,0:2:3:0,3,26 0/0:6,1:7:6:0,6,49 1 10694 . C G 85.78 . AC=4;AF=1.00;AN=4;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=17.21;MQ0=17;QD=8.58 GT:AD:DP:GQ:PL ./. ./. 1/1:2,3:5:6:74,6,0 1/1:3,2:5:3:35,3,0 ./. ./. ./. 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL ./. ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33 1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417 1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128 1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079 1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596 1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921 1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230 1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767 1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677 1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178 GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86 1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310 1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620 1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326 1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003 1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055 1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934 1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861 1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246 1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193 1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827 1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895 1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285 1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472 1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706 1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760 1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641 bio-vcf-0.9.5/test/data/regression/thread4_4.ref000066400000000000000000000616101400124230400213700ustar00rootroot00000000000000##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550 1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296 GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344 1 10665 . C G 56.61 . AC=2;AF=0.250;AN=8;BaseQRankSum=2.219;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=25.41;MQ0=15;MQRankSum=0.185;QD=4.72;ReadPosRankSum=1.849 GT:AD:DP:GQ:PL ./. ./. 0/1:4,3:7:57:57,0,78 0/1:3,2:5:23:30,0,23 ./. 0/0:2,0:2:3:0,3,26 0/0:6,1:7:6:0,6,49 1 10694 . C G 85.78 . AC=4;AF=1.00;AN=4;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=17.21;MQ0=17;QD=8.58 GT:AD:DP:GQ:PL ./. ./. 1/1:2,3:5:6:74,6,0 1/1:3,2:5:3:35,3,0 ./. ./. ./. 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL ./. ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33 1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417 1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128 1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079 1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596 1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921 1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230 1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767 1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677 1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178 GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86 1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310 1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620 1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326 1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003 1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055 1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934 1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861 1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246 1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193 1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827 1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895 1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285 1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472 1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706 1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760 1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641 bio-vcf-0.9.5/test/data/regression/thread4_4_failed_filter-stderr.ref000066400000000000000000000003751400124230400255430ustar00rootroot00000000000000Unknown field name in record, did you mean r.info.t? Unknown field name in record, did you mean r.info.t? Unknown field name in record, did you mean r.info.t? Unknown field name in record, did you mean r.info.t? ERROR: execution expired bio-vcf-0.9.5/test/data/regression/vcf2json_full_header.ref000066400000000000000000000411321400124230400236730ustar00rootroot00000000000000 { "HEADER": { "files": [], }, "COLUMNS": ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT","Original","s1t1","s2t1","s3t1","s1t2","s2t2","s3t2"], "META": {"INFO":{"AC":{"ID":"AC","Number":"A","Type":"Integer","Description":"Allele count in genotypes, for each ALT allele, in the same order as listed"},"AF":{"ID":"AF","Number":"A","Type":"Float","Description":"Allele Frequency, for each ALT allele, in the same order as listed"},"AN":{"ID":"AN","Number":"1","Type":"Integer","Description":"Total number of alleles in called genotypes"},"BaseQRankSum":{"ID":"BaseQRankSum","Number":"1","Type":"Float","Description":"Z-score from Wilcoxon rank sum test of Alt Vs. 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[142,28], "DP": 170, "GQ": 91, "GT": "0/1", "PL": [91,0,2919] } , "s3t1": { "AD": [160,40], "DP": 200, "GQ": 99, "GT": "0/1", "PL": [499,0,2815] } , "s1t2": { "AD": [109,17], "DP": 126, "GQ": 99, "GT": "0/1", "PL": [167,0,2363] } , "s2t2": { "AD": [111,34], "DP": 145, "GQ": 99, "GT": "0/1", "PL": [554,0,2268] } , "s3t2": { "AD": [141,38], "DP": 179, "GQ": 99, "GT": "0/1", "PL": [277,0,2827] } } }, { "seq:chr": "1" , "seq:pos": 15211 , "seq:ref": "T" , "seq:alt": "G" , "dp": 992 , "samples" : { "Original": { "AD": [19,35], "DP": 54, "GQ": 99, "GT": "0/1", "PL": [858,0,183] } , "s1t1": { "AD": [63,120], "DP": 183, "GQ": 99, "GT": "0/1", "PL": [2771,0,960] } , "s2t1": { "AD": [50,111], "DP": 161, "GQ": 99, "GT": "0/1", "PL": [2213,0,740] } , "s3t1": { "AD": [58,113], "DP": 171, "GQ": 99, "GT": "0/1", "PL": [2326,0,685] } , "s1t2": { "AD": [39,81], "DP": 120, "GQ": 99, "GT": "0/1", "PL": [1707,0,678] } , "s2t2": { "AD": [38,96], "DP": 134, "GQ": 99, "GT": "0/1", "PL": [2126,0,499] } , "s3t2": { "AD": [61,107], "DP": 168, "GQ": 99, "GT": "0/1", "PL": [2071,0,895] } } }, { "seq:chr": "1" , "seq:pos": 15274 , "seq:ref": "A" , "seq:alt": "G" , "dp": 636 , "samples" : { "Original": { "AD": [1,14,22], "DP": 37, "GQ": 99, "GT": "1/2", "PL": [717,494,467,224,0,170] } , "s1t1": { "AD": [1,45,75], "DP": 121, "GQ": 99, "GT": "1/2", "PL": [1922,1334,1265,588,0,441] } , "s2t1": { "AD": [0,31,71], "DP": 102, "GQ": 99, "GT": "1/2", "PL": [1960,1563,1515,396,0,222] } , "s3t1": { "AD": [1,59,77], "DP": 137, "GQ": 99, "GT": "1/2", "PL": [2009,1376,1298,633,0,486] } , "s1t2": { "AD": [0,18,52], "DP": 71, "GQ": 62, "GT": "1/2", "PL": [938,789,771,149,0,62] } , "s2t2": { "AD": [0,29,38], "DP": 67, "GQ": 99, "GT": "1/2", "PL": [1141,883,853,258,0,162] } , "s3t2": { "AD": [0,38,60], "DP": 98, "GQ": 99, "GT": "1/2", "PL": [1464,1064,1016,399,0,285] } } }, { "seq:chr": "1" , "seq:pos": 15447 , "seq:ref": "A" , "seq:alt": "G" , "dp": 1213 , "samples" : { "Original": { "AD": [42,4], "DP": 46, "GQ": 34, "GT": "0/0", "PL": [0,34,690] } , "s1t1": { "AD": [220,22], "DP": 242, "GQ": 99, "GT": "0/0", "PL": [0,99,3639] } , "s2t1": { "AD": [167,16], "DP": 183, "GQ": 42, "GT": "0/0", "PL": [0,42,2582] } , "s3t1": { "AD": [201,25], "DP": 226, "GQ": 78, "GT": "0/1", "PL": [78,0,2854] } , "s1t2": { "AD": [121,16], "DP": 137, "GQ": 39, "GT": "0/1", "PL": [39,0,1877] } , "s2t2": { "AD": [160,13], "DP": 173, "GQ": 99, "GT": "0/0", "PL": [0,139,2724] } , "s3t2": { "AD": [157,18], "DP": 175, "GQ": 34, "GT": "0/1", "PL": [34,0,2472] } } }, { "seq:chr": "1" , "seq:pos": 15688 , "seq:ref": "C" , "seq:alt": "T" , "dp": 904 , "samples" : { "Original": { "AD": [34,3], "DP": 37, "GQ": 15, "GT": "0/0", "PL": [0,15,335] } , "s1t1": { "AD": [166,16], "DP": 182, "GQ": 61, "GT": "0/0", "PL": [0,61,2190] } , "s2t1": { "AD": [131,16], "DP": 147, "GQ": 69, "GT": "0/1", "PL": [69,0,1563] } , "s3t1": { "AD": [167,17], "DP": 184, "GQ": 22, "GT": "0/1", "PL": [22,0,1894] } , "s1t2": { "AD": [88,12], "DP": 100, "GQ": 15, "GT": "0/0", "PL": [0,15,1099] } , "s2t2": { "AD": [88,13], "DP": 101, "GQ": 1, "GT": "0/0", "PL": [0,1,1126] } , "s3t2": { "AD": [132,16], "DP": 148, "GQ": 18, "GT": "0/0", "PL": [0,18,1706] } } }, { "seq:chr": "1" , "seq:pos": 16068 , "seq:ref": "T" , "seq:alt": "C" , "dp": 398 , "samples" : { "Original": { "AD": [18,15], "DP": 33, "GQ": 99, "GT": "0/1", "PL": [182,0,404] } , "s1t1": { "AD": [51,6], "DP": 57, "GQ": 31, "GT": "0/0", "PL": [0,31,815] } , "s2t1": { "AD": [52,16], "DP": 68, "GQ": 64, "GT": "0/1", "PL": [64,0,1101] } , "s3t1": { "AD": [68,13], "DP": 81, "GQ": 99, "GT": "0/0", "PL": [0,99,1505] } , "s1t2": { "AD": [41,8], "DP": 49, "GQ": 51, "GT": "0/0", "PL": [0,51,1010] } , "s2t2": { "AD": [40,9], "DP": 49, "GQ": 21, "GT": "0/1", "PL": [21,0,702] } , "s3t2": { "AD": [38,19], "DP": 58, "GQ": 99, "GT": "0/1", "PL": [153,0,760] } } }, { "seq:chr": "1" , "seq:pos": 16103 , "seq:ref": "T" , "seq:alt": "G" , "dp": 526 , "samples" : { "Original": { "AD": [21,29], "DP": 50, "GQ": 99, "GT": "0/1", "PL": [504,0,450] } , "s1t1": { "AD": [55,24], "DP": 79, "GQ": 99, "GT": "0/1", "PL": [209,0,838] } , "s2t1": { "AD": [49,37], "DP": 86, "GQ": 99, "GT": "0/1", "PL": [456,0,1002] } , "s3t1": { "AD": [74,32], "DP": 106, "GQ": 99, "GT": "0/1", "PL": [193,0,1519] } , "s1t2": { "AD": [41,19], "DP": 60, "GQ": 99, "GT": "0/1", "PL": [141,0,740] } , "s2t2": { "AD": [38,23], "DP": 61, "GQ": 99, "GT": "0/1", "PL": [257,0,548] } , "s3t2": { "AD": [38,46], "DP": 84, "GQ": 99, "GT": "0/1", "PL": [628,0,641] } } }, ] }bio-vcf-0.9.5/test/performance/000077500000000000000000000000001400124230400163205ustar00rootroot00000000000000bio-vcf-0.9.5/test/performance/metrics.md000066400000000000000000000123071400124230400203130ustar00rootroot00000000000000Round of testing on Macbook PRO running Linux with Intel(R) Core(TM) i5-3210M CPU @ 2.50GHz and ruby -v ruby 2.1.0p0 (2013-12-25 revision 44422) [x86_64-linux] wc test/tmp/test.vcf 12469 137065 2053314 test/tmp/test.vcf time ./bin/bio-vcf -i --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null vcf 0.0.3-pre4 (biogem Ruby 2.1.0) by Pjotr Prins 2014 Options: {:show_help=>false, :ignore_missing=>true, :filter=>"r.info.dp>20", :sfilter=>"s.dp>10"} real 0m1.215s user 0m1.208s sys 0m0.004s Reload time ./bin/bio-vcf -i --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null vcf 0.0.3-pre4 (biogem Ruby 2.1.0) by Pjotr Prins 2014 Options: {:show_help=>false, :ignore_missing=>true, :filter=>"r.info.dp>20", :sfilter=>"s.dp>10"} real 0m1.194s user 0m1.172s sys 0m0.016s Introduced method caching real 0m1.190s user 0m1.180s sys 0m0.004s Introduce !!Float test real 0m1.187s user 0m1.180s sys 0m0.004s Cache sample index real 0m1.156s user 0m1.148s sys 0m0.004s Run the profiler ruby -rprofile ./bin/bio-vcf -i --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null vcf 0.0.3-pre4 (biogem Ruby 2.1.0) by Pjotr Prins 2014 Options: {:show_help=>false, :ignore_missing=>true, :filter=>"r.info.dp>20", :sfilter=>"s.dp>10"} % cumulative self self total time seconds seconds calls ms/call ms/call name 9.45 2.19 2.19 34968 0.06 0.76 Object#parse_line 7.25 3.87 1.68 75031 0.02 0.03 BioVcf::VcfRecordInfo#[]= 7.12 5.52 1.65 34968 0.05 0.29 Kernel.eval 6.86 7.11 1.59 87481 0.02 0.10 BioVcf::VcfRecordInfo#initialize 5.57 8.40 1.29 35994 0.04 0.47 Array#each 4.14 9.36 0.96 34253 0.03 0.65 BioVcf::VcfRecord#each_sample 3.93 10.27 0.91 93880 0.01 0.03 BioVcf::VcfRecordParser.get_format 3.88 11.17 0.90 145920 0.01 0.01 String#split Late parsing of info field without split: real 0m1.124s user 0m1.120s sys 0m0.008s Global sample info caching real 0m1.032s user 0m1.020s sys 0m0.008s Assign some repeated Hash queries real 0m1.028s user 0m1.024s sys 0m0.000s Profiler now picking out eval for further optimization % cumulative self self total time seconds seconds calls ms/call ms/call name 10.45 1.80 1.80 34968 0.05 0.59 Object#parse_line 7.89 3.16 1.36 34968 0.04 0.17 Kernel.eval 5.69 4.14 0.98 34253 0.03 0.57 BioVcf::VcfRecord#each_sample 4.93 4.99 0.85 12497 0.07 1.37 nil# Compiling sample eval real 0m0.820s user 0m0.812s sys 0m0.004s Compiling record eval real 0m0.647s user 0m0.644s sys 0m0.000s Walk examples by index, rather than by name real 0m0.612s user 0m0.596s sys 0m0.012s More caching real 0m0.600s user 0m0.592s sys 0m0.004s And the latest profiling % cumulative self self total time seconds seconds calls ms/call ms/call name 12.98 2.02 2.02 34968 0.06 0.51 Object#parse_line 7.78 3.23 1.21 22518 0.05 0.14 BioVcf::VcfRecord#sample_by_index 5.59 4.10 0.87 34253 0.03 0.47 BioVcf::VcfRecord#each_sample 4.82 4.85 0.75 34968 0.02 0.03 BioVcf::ConvertStringToValue.integer? 4.50 5.55 0.70 12450 0.06 0.13 BioVcf::VcfRecordInfo#method_missing 4.31 6.22 0.67 69974 0.01 0.03 Class#new 4.24 6.88 0.66 12499 0.05 1.23 nil# 3.79 7.47 0.59 12450 0.05 0.06 BioVcf::VcfLine.parse Introduced --num-threads time ./bin/bio-vcf -i --num-threads --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null on a dual-core running Linux real 0m0.389s user 0m1.132s sys 0m0.148s Latest time ./bin/bio-vcf -i --num-threads 4 --thread-lines 2000 --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null vcf 0.8.3-pre1 (biogem Ruby 2.1.0) by Pjotr Prins 2014 Options: {:show_help=>false, :source=>"https://github.com/CuppenResearch/bioruby-vcf", :version=>"0.8.3-pre1 (Pjotr Prins)", :date=>"2014-12-31 13:30:32 +0300", :thread_lines=>2000, :ignore_missing=>true, :num_threads=>4, :filter=>"r.info.dp>20", :sfilter=>"s.dp>10"} real 0m0.600s user 0m1.472s sys 0m0.068s Profiling: . % cumulative self self total time seconds seconds calls ms/call ms/call name 15.01 3.23 3.23 34968 0.09 0.82 Object#parse_line 8.22 5.00 1.77 22518 0.08 0.22 BioVcf::VcfRecord#sample_by_index 4.97 6.07 1.07 22518 0.05 0.27 BioVcf::VcfSample::Sample#sfilter bio-vcf-0.9.5/test/stress/000077500000000000000000000000001400124230400153425ustar00rootroot00000000000000bio-vcf-0.9.5/test/stress/stress_test.sh000077500000000000000000000012621400124230400202640ustar00rootroot00000000000000#! /bin/bash # # Stress test bio-vcf by running it on large files and comparing # results using threads input=test/data/input/multisample.vcf filter='--sfilter 's.dp>70' --seval s.dp' echo "cat $input | ./bin/bio-vcf --num-threads 1 $filter > stress_simple01.vcf" cat $input | ./bin/bio-vcf --num-threads 1 $filter > stress_simple01.vcf cat $input | ./bin/bio-vcf --num-threads 2 $filter > stress_simple02.vcf cat $input | ./bin/bio-vcf --num-threads 4 $filter > stress_simple03.vcf cat $input | ./bin/bio-vcf $filter > stress_simple04.vcf cat $input | ./bin/bio-vcf --thread-lines 3 $filter > stress_simple05.vcf cat $input | ./bin/bio-vcf --thread-lines 1 $filter > stress_simple06.vcf bio-vcf-0.9.5/test2.vcf000066400000000000000000000000001400124230400145670ustar00rootroot00000000000000