Mercurial > repos > iuc > tb_variant_filter
changeset 0:3b1e7c170b10 draft
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
| author | iuc |
|---|---|
| date | Thu, 10 Oct 2019 17:59:02 -0400 |
| parents | |
| children | eee2da03d1f5 |
| files | tb_variant_filter.xml test-data/test_input1.vcf test-data/test_input2.vcf test-data/test_output1.vcf test-data/test_output2.vcf test-data/test_output3.vcf test-data/test_output4.vcf test-data/test_output5.vcf test-data/test_output6.vcf |
| diffstat | 9 files changed, 866 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tb_variant_filter.xml Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,160 @@ +<tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="16.04"> + <description>M. tuberculosis H37Rv VCF filter</description> + <macros> + <token name="@TOOL_VERSION@">0.1.3</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + tb_variant_filter + #if "region_filter" in str($filters).split(',') + #if str($filter_options.show_filter_options) == "yes": + --region_filter $filter_options.region_filter + #else + --region_filter pe_ppe,uvp + #end if + #end if + #if "close_to_indel_filter" in str($filters).split(',') + --close_to_indel_filter + #if str($filter_options.show_filter_options) == "yes": + --indel_window_size $filter_options.indel_window_size + #end if + #end if + #if "min_percentage_alt_filter" in str($filters).split(',') + --min_percentage_alt_filter + #if str($filter_options.show_filter_options) == "yes": + --min_percentage_alt $filter_options.min_percentage_alt + #end if + #end if + #if "min_depth_filter" in str($filters).split(',') + --min_depth_filter + #if str($filter_options.show_filter_options) == "yes": + --min_depth $filter_options.min_depth + #end if + #end if + #if "snv_only_filter" in str($filters).split(','): + --snv_only_filter + #end if + '$input1' '$output1' + ]]></command> + <inputs> + <param type="data" name="input1" label="VCF file to be filter" format="vcf"/> + + <param type="select" name="filters" multiple="true" label="Filters to apply"> + <option value="region_filter" selected="true">Filter out variants by regions</option> + <option value="close_to_indel_filter">Filter variants close to indels</option> + <option value="min_percentage_alt_filter">Filter variants by percentage alt allele</option> + <option value="min_depth_filter">Filter sites by read alignment depth</option> + <option value="snv_only_filter">Only accept SNVs</option> + </param> + + <conditional name="filter_options"> + <param type="select" name="show_filter_options" label="Show options for the filters"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable"> + <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here --> + <option value="pe_ppe" selected="true">PE/PPE</option> + <option value="tbprofiler">TBProfiler antibiotic resistant genes</option> + <option value="mtbseq">MTBseq antibiotic resistant genes</option> + <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option> + </param> + <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/> + <param argument="--min_percentage_alt" type="float" value="90" + label="Minimum alternate allele percentage to accept"/> + <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/> + </when> + <when value="no"></when> + + </conditional> + </inputs> + <outputs> + <data name="output1" format="vcf"/> + </outputs> + <tests> + <test> + <param name="input1" value="test_input1.vcf" ftype="vcf" /> + <param name="filters" value="region_filter" /> + <conditional name="filter_options"> + <param name="show_filter_options" value="yes" /> + <param name="region_filter" value="pe_ppe,tbprofiler,uvp" /> + </conditional> + <output name="output1" file="test_output1.vcf" ftype="vcf" /> + </test> + <test> + <param name="input1" value="test_input1.vcf" ftype="vcf" /> + <param name="filters" value="close_to_indel_filter" /> + <conditional name="filter_options"> + <param name="show_filter_options" value="yes" /> + <param name="indel_window_size" value="5" /> + </conditional> + <output name="output1" file="test_output2.vcf" ftype="vcf" /> + </test> + <test> + <param name="input1" value="test_input1.vcf" ftype="vcf" /> + <param name="filters" value="min_percentage_alt_filter" /> + <conditional name="filter_options"> + <param name="show_filter_options" value="yes" /> + <param name="min_percentage_alt" value="95.0" /> + </conditional> + <output name="output1" file="test_output3.vcf" ftype="vcf" /> + </test> + <test> + <param name="input1" value="test_input2.vcf" ftype="vcf" /> + <param name="filters" value="min_percentage_alt_filter" /> + <conditional name="filter_options"> + <param name="show_filter_options" value="yes" /> + <param name="min_percentage_alt" value="30.0" /> + </conditional> + <output name="output1" file="test_output4.vcf" ftype="vcf" /> + </test> + <test> + <param name="input1" value="test_input1.vcf" ftype="vcf" /> + <param name="filters" value="min_depth_filter" /> + <conditional name="filter_options"> + <param name="show_filter_options" value="yes" /> + <param name="min_depth" value="30" /> + </conditional> + <output name="output1" file="test_output5.vcf" ftype="vcf" /> + </test> + <test> + <param name="input1" value="test_input1.vcf" ftype="vcf" /> + <param name="filters" value="snv_only_filter" /> + <output name="output1" file="test_output6.vcf" ftype="vcf" /> + </test> + </tests> + <help><![CDATA[ +This tool offers multiple options for filtering variants (in +VCF files, relative to M. tuberculosis H37Rv). + +It currently has 5 main modes: + +1. Filter by region. Mask out variants in certain regions. Region lists available as: + 1. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_ + 2. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes + 3. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes + 4. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome +2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site. +3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles. +4. Filter by depth of aligned reads. +5. Filter out all variants that are not SNV (single nucleotide variants). + +When used together the effects of the filters are added (i.e. a variant is masked out if it is masked by any of the filters). + ]]></help> + <citations> + <citation type="bibtex"><![CDATA[ +@misc{vanHeusden2019, + author = {van Heusden, P.}, + title = {tb_variant_filter}, + year = {2019}, + publisher = {GitHub}, + journal = {GitHub repository}, + howpublished = {\url{https://github.com/pvanheus/tb_variant_filter}}, + commit = {4a9b2a4a85ddbfbb0d713a02373c8aa0aa159a6c} +} + ]]></citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_input1.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,102 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20190323 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig=<ID=Chromosome,length=4411532> +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044" +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out +Chromosome 1849 . C A 3412.24 . AB=0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:0:0:110:3850:-346.644,-33.1133,0 +Chromosome 1977 . A G 3234.43 . AB=0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3704:-333.508,-31.9092,0 +Chromosome 4013 . T C 3965.91 . AB=0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:125:4448:-400.411,-37.6288,0 +Chromosome 7362 . G C 4009.71 . AB=0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4518:-406.711,-37.9298,0 +Chromosome 9304 . G A 4222.23 . AB=0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4764:-428.865,-40.9401,0 +Chromosome 11820 . C G 2252.54 . AB=0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:74:0:0:74:2662:-239.791,-22.2762,0 +Chromosome 11879 . A G 1815.99 . AB=0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:63:0:0:63:2212:-199.306,-18.9649,0 +Chromosome 14785 . T C 4342.4 . AB=0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:139:4874:-438.763,-41.8432,0 +Chromosome 14861 . G T 4237.79 . AB=0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:135:0:0:133:4758:-427.969,-40.037,0 +Chromosome 15117 . C G 3298.26 . AB=0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3708:-333.903,-31.9092,0 +Chromosome 15890 . G A 3349.13 . AB=0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:116:3770:-339.321,-34.9195,0 +Chromosome 16119 . C A 3794.09 . AB=0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:124:4268:-383.905,-37.3277,0 +Chromosome 21795 . G A 768.571 . AB=0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:28:0:0:28:892:-80.5646,-8.42884,0 +Chromosome 25610 . G C 2779.82 . AB=0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3137:-282.515,-26.7917,0 +Chromosome 26959 . C G 2791.1 . AB=0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:91:0:0:91:3152:-283.856,-27.3937,0 +Chromosome 27455 . T C 1646.76 . AB=0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:52:0:0:52:1868:-168.374,-15.6536,0 +Chromosome 28366 . AT A 2447.14 . AB=0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:82:2764:-248.651,-24.6845,0 +Chromosome 34044 . T C 3866.76 . AB=0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4351:-391.712,-36.7257,0 +Chromosome 36008 . G C 2942.73 . AB=0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:0:0:98:3356:-301.935,-29.5009,0 +Chromosome 37031 . C G 3922.6 . AB=0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:129:1:34:128:4437:-396.072,-35.434,0 +Chromosome 37305 . C G 4975.87 . AB=0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:5577:-501.976,-47.2617,0 +Chromosome 39158 . C G 2017.05 . AB=0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:66:0:0:66:2297:-206.967,-19.868,0 +Chromosome 42281 . C A 996.941 . AB=0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:33:0:0:33:1179:-106.407,-9.93399,0 +Chromosome 42967 . G C 2851.59 . AB=0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3244:-292.146,-27.6948,0 +Chromosome 43347 . T C 2847.24 . AB=0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3233:-291.161,-27.6948,0 +Chromosome 44768 . A G 3099.48 . AB=0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:99:3501:-315.241,-29.802,0 +Chromosome 49360 . C T 2971.13 . AB=0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:97:0:0:97:3365:-303.059,-29.1999,0 +Chromosome 49690 . GCC G 3479.85 . AB=0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:117:3917:-352.709,-35.2205,0 +Chromosome 50557 . T C 3743.4 . AB=0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4203:-378.409,-36.4246,0 +Chromosome 51949 . A G 3521.52 . AB=0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:112:0:0:112:3955:-356.092,-33.7154,0 +Chromosome 54394 . A G 3304.32 . AB=0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:104:3711:-333.937,-31.3071,0 +Chromosome 62049 . A G 2249.46 . AB=0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:1:35:77:2659:-236.018,-19.9817,0 +Chromosome 63146 . G T 5120.15 . AB=0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:5737:-516.376,-49.0679,0 +Chromosome 65150 . C T 4046.85 . AB=0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:134:0:0:134:4538:-408.565,-40.338,0 +Chromosome 65246 . C T 3297.8 . AB=0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:107:0:0:106:3712:-334.038,-31.9092,0 +Chromosome 68337 . T TC 1791.13 . AB=0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:60:2038:-183.378,-18.0618,0 +Chromosome 69989 . G A 3539.46 . AB=0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:119:0:0:119:3973:-357.725,-35.8226,0 +Chromosome 70267 . G T 3018.85 . AB=0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:1:25:100:3421:-305.576,-27.9042,0 +Chromosome 70816 . A G 4198.57 . AB=0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4707:-423.747,-40.9401,0 +Chromosome 71336 . G C 556.161 . AB=0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:21:0:0:21:770:-69.6143,-6.32163,0 +Chromosome 71914 . T C 3905.06 . AB=0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4382:-394.523,-37.9298,0 +Chromosome 75233 . C A 1903.61 . AB=0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2172:-195.723,-19.2659,0 +Chromosome 75940 . G C 2674.83 . AB=0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3048:-274.519,-26.7917,0 +Chromosome 87468 . C T 4061.4 . AB=0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4584:-412.628,-37.9298,0 +Chromosome 92199 . T G 686.38 . AB=0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:799:-72.2155,-6.92369,0 +Chromosome 94388 . G A 2922.87 . AB=0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:95:0:0:95:3292:-296.486,-28.5979,0 +Chromosome 99162 . TCGGTGTGCG T 2040.99 . AB=0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2358:-212.453,-23.4803,0 +Chromosome 105139 . C A 3418.74 . AB=0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:1:38:109:3888:-346.257,-29.316,0 +Chromosome 105736 . T C 1805.18 . AB=0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:61:2101:-189.335,-18.3628,0 +Chromosome 116000 . T G 3196.37 . AB=0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3605:-324.628,-31.6082,0 +Chromosome 122109 . A G 3324.29 . AB=0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:111:0:0:111:3735:-336.329,-33.4143,0 +Chromosome 123454 . C T 4362.28 . AB=0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:136:4894:-440.321,-40.9401,0 +Chromosome 123520 . T C 3793.13 . AB=0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4262:-383.682,-36.4246,0 +Chromosome 125711 . GGTT G 3140.7 . AB=0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3531:-317.98,-31.6082,0 +Chromosome 125830 . G GA 2079.98 . AB=0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:69:2347:-211.164,-20.7711,0 +Chromosome 131174 . T TG 2854.04 . AB=0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:97:3213:-288.972,-29.1999,0 +Chromosome 133839 . C T 2457.55 . AB=0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2802:-252.374,-23.4803,0 +Chromosome 134024 . T C 2242.53 . AB=0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2543:-229.099,-21.6742,0 +Chromosome 138419 . G A 4166.36 . AB=0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:132:0:0:132:4683:-421.582,-39.736,0 +Chromosome 139297 . G T 3706.81 . AB=0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:120:0:0:120:4165:-374.978,-36.1236,0 +Chromosome 143207 . T C 2180.95 . AB=0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2523:-227.3,-21.6742,0 +Chromosome 146087 . T C 4315.28 . AB=0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:137:4844:-436.07,-41.2411,0 +Chromosome 147262 . G T 3766.49 . AB=0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4228:-380.649,-36.7257,0 +Chromosome 154283 . T C 4403.08 . AB=0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:141:0:0:141:4941:-444.791,-42.4452,0 +Chromosome 154990 . G T 4207.92 . AB=0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:143:0:0:142:4724:-424.969,-42.7463,0 +Chromosome 162151 . GT G 2208.67 . AB=0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:81:2524:-226.95,-24.3834,0 +Chromosome 163940 . A G 2507.97 . AB=0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:80:0:0:80:2839:-255.719,-24.0824,0 +Chromosome 166253 . A C 3141.13 . AB=0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:102:0:0:102:3586:-322.902,-30.7051,0 +Chromosome 177857 . G A 2984.02 . AB=0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:98:0:0:98:3389:-305.192,-29.5009,0 +Chromosome 188800 . T C 1887.67 . AB=0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2217:-199.772,-19.2659,0 +Chromosome 190816 . A C 1715.49 . AB=0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:57:0:0:57:2026:-182.579,-17.1587,0 +Chromosome 194305 . C CGG 1602.78 . AB=0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:59:0:0:58:1889:-169.924,-17.4597,0 +Chromosome 2738274 . A C 511.15 . AB=0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:19:1:35:18:633:-53.7923,-2.22094,0 +Chromosome 3750185 . CGAC GGTG 1102.73 . AB=0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex GT:DP:RO:QR:AO:QA:GL 1/1:36:0:0:36:1255:-113.24,-10.8371,0 +Chromosome 3750193 . G A 1198.75 . AB=0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1367:-123.307,-12.0412,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_input2.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,60 @@ +##fileformat=VCFv4.1 +##fileDate=20150301 +##source=freeBayes v0.9.20-16-g3e35e72 +##reference=reference.fasta +##phasing=none +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=technology.Illumina,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from Illumina"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BR_002 BR_004 BR_006 BR_009 BR_013 BR_015 BR_016 BR_021 BR_023 BR_024 BR_025 BR_028 BR_030 BR_031 BR_040 BR_041 BR_043 BR_046 BR_047 BR_048 WL_031 WL_032 WL_054 WL_056 WL_057 WL_058 WL_061 WL_064 WL_066 WL_067 WL_069 WL_070 WL_071 WL_072 WL_076 WL_077 WL_078 WL_079 WL_080 WL_081 +E2_L101 117 . GG AT 12920.7 . AB=0.47191;ABP=4.84019;AC=6;AF=0.0810811;AN=74;AO=127;CIGAR=2X;DP=1915;DPB=1915;DPRA=1.03669;EPP=278.787;EPPR=3870.4;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=37;NUMALT=1;ODDS=8.14286;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4199;QR=57663;RO=1781;RPL=0;RPP=278.787;RPPR=3870.4;RPR=127;RUN=1;SAF=0;SAP=278.787;SAR=127;SRF=0;SRP=3870.4;SRR=1781;TYPE=mnp;technology.Illumina=1 GT:DP:RO:QR:AO:QA:GL 0/1:63:34:1128:29:947:-298.563,0,-354.855 0/0:275:274:8575:0:0:0,-82.4822,-2963.46 0/0:16:16:550:0:0:0,-4.81648,-177.826 0/0:50:50:1549:0:0:0,-15.0515,-539.68 . 0/0:137:136:4316:0:0:0,-40.9401,-1476.57 0/0:15:15:517:0:0:0,-4.51545,-166.858 0/0:63:62:2127:0:0:0,-18.6639,-687.592 0/1:5:2:69:3:104:-32.1979,0,-21.0475 0/0:13:13:401:0:0:0,-3.91339,-140.389 0/0:21:21:682:0:0:0,-6.32163,-229.683 0/0:32:32:1082:0:0:0,-9.63296,-353.685 . 0/0:25:25:833:0:0:0,-7.52575,-275.278 0/0:45:45:1363:0:0:0,-13.5463,-482.942 0/0:39:39:1253:0:0:0,-11.7402,-425.057 0/0:49:49:1491:0:0:0,-14.7505,-526.459 0/0:14:14:436:0:0:0,-4.21442,-151.539 0/0:82:81:2406:0:0:0,-24.3834,-864.723 0/1:27:13:421:14:448:-144.499,0,-134.074 0/0:68:68:2110:0:0:0,-20.47,-734.156 0/0:16:16:518:0:0:0,-4.81648,-174.927 0/0:56:56:1847:0:0:0,-16.8577,-614.506 0/0:34:34:1160:0:0:0,-10.235,-376.705 0/1:25:16:551:9:311:-92.7994,0,-170.391 0/0:52:51:1692:0:0:0,-15.3525,-560.486 0/0:33:33:1085:0:0:0,-9.93399,-361.947 0/0:21:21:709:0:0:0,-6.32163,-232.126 0/0:106:105:3327:1:29:0,-21.0095,-1128.75 0/0:9:9:310:0:0:0,-2.70927,-100.234 0/0:22:22:716:0:0:0,-6.62266,-240.745 0/0:129:128:4337:0:0:0,-38.5318,-1414.47 0/0:149:148:4978:0:0:0,-44.5524,-1632.14 0/0:26:26:837:0:0:0,-7.82678,-283.629 . 0/0:7:7:237:0:0:0,-2.10721,-77.6617 0/0:13:13:429:0:0:0,-3.91339,-142.928 0/1:126:63:2125:63:2117:-656.871,0,-657.593 0/1:21:13:446:8:243:-79.8453,0,-138.147 0/0:31:31:1050:0:0:0,-9.33193,-342.807 +E2_L101 123 . T A 688.632 . AB=0.411765;ABP=4.1599;AC=1;AF=0.0135135;AN=74;AO=7;CIGAR=1X;DP=1922;DPB=1922;DPRA=0.32126;EPP=18.2106;EPPR=4159.21;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=37;NUMALT=1;ODDS=8.46314;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=239;QR=63119;RO=1914;RPL=0;RPP=18.2106;RPPR=4159.21;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=0;SRP=4159.21;SRR=1914;TYPE=snp;technology.Illumina=1 GT:DP:RO:QR:AO:QA:GL 0/0:63:63:2133:0:0:0,-18.9649,-696.24 0/0:275:274:8643:0:0:0,-82.4822,-2969.78 0/1:17:10:345:7:239:-72.7264,0,-106.266 0/0:50:50:1547:0:0:0,-15.0515,-539.5 . 0/0:137:137:4441:0:0:0,-41.2411,-1495.87 0/0:15:15:524:0:0:0,-4.51545,-167.491 0/0:63:63:2185:0:0:0,-18.9649,-700.918 0/0:5:5:152:0:0:0,-1.50515,-53.9786 0/0:13:13:429:0:0:0,-3.91339,-142.925 0/0:21:21:703:0:0:0,-6.32163,-231.577 0/0:32:32:1093:0:0:0,-9.63296,-354.673 . 0/0:25:25:869:0:0:0,-7.52575,-278.526 0/0:45:45:1355:0:0:0,-13.5463,-482.221 0/0:39:39:1328:0:0:0,-11.7402,-431.808 0/0:49:49:1561:0:0:0,-14.7505,-532.757 0/0:14:14:444:0:0:0,-4.21442,-152.263 0/0:82:82:2552:0:0:0,-24.6845,-885.917 0/0:27:27:861:0:0:0,-8.12781,-293.786 0/0:68:68:2195:0:0:0,-20.47,-741.8 0/0:16:16:548:0:0:0,-4.81648,-177.639 0/0:57:57:1937:0:0:0,-17.1587,-630.601 0/0:34:34:1191:0:0:0,-10.235,-379.496 0/0:25:25:869:0:0:0,-7.52575,-278.526 0/0:53:53:1791:0:0:0,-15.9546,-585.47 0/0:33:33:1143:0:0:0,-9.93399,-367.175 0/0:21:21:734:0:0:0,-6.32163,-234.383 0/0:106:106:3423:0:0:0,-31.9092,-1156.28 0/0:9:9:310:0:0:0,-2.70927,-100.234 0/0:22:22:757:0:0:0,-6.62266,-244.448 0/0:130:130:4441:0:0:0,-39.1339,-1439.89 0/0:151:151:5081:0:0:0,-45.4555,-1665.48 0/0:26:26:899:0:0:0,-7.82678,-289.224 . 0/0:7:7:244:0:0:0,-2.10721,-78.2996 0/0:13:13:445:0:0:0,-3.91339,-144.377 0/0:127:127:4180:0:0:0,-38.2308,-1392.41 0/0:21:21:712:0:0:0,-6.32163,-232.396 0/0:31:31:1054:0:0:0,-9.33193,-343.166 +E2_L101 125 . C T 110675 . AB=0.558397;ABP=37.7557;AC=47;AF=0.635135;AN=74;AO=1064;CIGAR=1X;DP=1923;DPB=1923;DPRA=0.800123;EPP=2313.46;EPPR=1866.13;GTI=0;LEN=1;MEANALT=1.02941;MQM=60;MQMR=60;NS=37;NUMALT=1;ODDS=7.31554;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32732;QR=26625;RO=858;RPL=0;RPP=2313.46;RPPR=1866.13;RPR=1064;RUN=1;SAF=0;SAP=2313.46;SAR=1064;SRF=0;SRP=1866.13;SRR=858;TYPE=snp;technology.Illumina=1 GT:DP:RO:QR:AO:QA:GL 0/1:63:29:919:34:1086:-351.067,0,-296.04 0/1:275:136:3998:139:4075:-1396.19,0,-1365.26 0/1:17:7:231:10:323:-104.267,0,-71.9963 0/0:50:50:1463:0:0:0,-15.0515,-531.939 . 0/1:137:73:2205:64:1932:-644.905,0,-741.47 0/1:15:6:206:9:301:-94.9006,0,-62.3614 0/1:63:14:477:49:1547:-512.541,0,-136.291 0/1:5:3:93:2:69:-21.0475,0,-31.1725 1/1:13:0:0:13:388:-139.212,-3.91339,0 1/1:21:0:0:21:616:-223.722,-6.32163,0 0/1:32:7:224:25:787:-261.493,0,-66.8418 . 1/1:25:0:0:25:815:-273.654,-7.52575,0 0/1:45:23:652:22:616:-218.165,0,-229.408 1/1:39:0:0:39:1185:-418.932,-11.7402,0 0/1:49:16:469:33:949:-334.932,0,-155.746 0/0:14:14:396:0:0:0,-4.21442,-147.916 1/1:82:0:0:82:2334:-866.31,-24.6845,0 0/1:27:14:431:13:389:-131.174,0,-142.961 1/1:68:0:0:68:2019:-725.97,-20.47,0 1/1:16:0:0:16:493:-172.669,-4.81648,0 0/1:57:2:58:55:1716:-577.549,0,-4.35015 1/1:34:0:0:34:1117:-372.828,-10.235,0 0/1:25:9:295:16:540:-169.396,0,-91.3433 0/1:53:26:837:27:880:-279.548,0,-267.677 1/1:33:0:0:33:1063:-359.964,-9.93399,0 0/1:21:12:397:9:297:-92.7309,0,-125.728 0/1:107:50:1484:57:1738:-580.482,0,-501.622 1/1:9:0:0:9:282:-97.6869,-2.70927,0 1/1:22:0:0:22:711:-240.294,-6.62266,0 0/1:130:57:1814:72:2337:-747.579,0,-580.516 0/0:151:150:4800:1:31:0,-34.3561,-1621.09 1/1:26:0:0:26:813:-281.46,-7.82678,0 . 1/1:7:0:0:7:223:-76.3831,-2.10721,0 1/1:13:0:0:13:425:-142.565,-3.91339,0 0/0:127:127:4112:0:0:0,-38.2308,-1386.3 0/1:21:12:387:9:297:-92.7307,0,-124.822 0/1:31:21:677:10:338:-101.416,0,-219.904 +E2_L101 189 . GT GA,AA 79493.6 . AB=0.530648,0.564103;ABP=12.3275,4.40227;AC=27,1;AF=0.364865,0.0135135;AN=74;AO=711,22;CIGAR=1M1X,2X;DP=1947;DPB=1947;DPRA=1.2223,0.775155;EPP=1546.93,50.7827;EPPR=2623.98;GTI=0;LEN=1,2;MEANALT=1.2,2;MQM=59.9536,60;MQMR=59.9528;NS=37;NUMALT=2;ODDS=8.57375;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=26768,823;QR=45917;RO=1207;RPL=711,22;RPP=1546.93,50.7827;RPPR=2623.98;RPR=0,0;RUN=1,1;SAF=0,0;SAP=1546.93,50.7827;SAR=711,22;SRF=0;SRP=2623.98;SRR=1207;TYPE=snp,mnp;technology.Illumina=1,1 GT:DP:RO:QR:AO:QA:GL 0/1:63:29:1128:33,0:1297,0:-362.019,0,-314.829,-370.749,-324.763,-695.435 0/1:279:136:5023:143,0:5199,0:-1527.93,0,-1456.1,-1568.87,-1499.14,-3067.65 0/0:18:18:720:0,0:0,0:0,-5.41854,-209.126,-5.41854,-209.126,-209.126 0/0:50:50:1802:0,0:0,0:0,-15.0515,-562.43,-15.0515,-562.43,-562.43 . 0/0:140:140:5188:0,0:0,0:0,-42.1442,-1586.93,-42.1442,-1586.93,-1586.93 0/0:15:15:612:0,0:0,0:0,-4.51545,-175.417,-4.51545,-175.417,-175.417 0/1:63:14:556:49,0:1902,0:-544.414,0,-143.417,-548.629,-158.168,-706.402 0/0:7:7:255:0,0:0,0:0,-2.10721,-79.294,-2.10721,-79.294,-79.294 1/1:13:0:0:13,0:486,0:-148.079,-3.91339,0,-148.079,-3.91339,-148.079 0/1:21:10:377:11,0:413,0:-119.194,0,-107.957,-122.204,-111.268,-233.097 0/1:33:7:283:26,0:969,0:-285.557,0,-71.9094,-287.664,-79.7362,-367.003 . 0/1:26:19:720:7,0:270,0:-72.8033,0,-209.291,-78.5229,-211.398,-289.538 0/0:45:45:1610:0,0:0,0:0,-13.5463,-505.167,-13.5463,-505.167,-505.167 1/2:39:0:0:17,22:633,823:-431.573,-243.764,-238.646,-188.182,0,-181.559 0/1:49:16:571:33,0:1209,0:-358.342,0,-164.964,-363.158,-174.898,-537.697 0/0:14:14:515:0,0:0,0:0,-4.21442,-158.684,-4.21442,-158.684,-158.684 0/1:82:37:1340:45,0:1616,0:-481.016,0,-392.198,-492.154,-405.744,-897.538 0/1:27:14:522:13,0:489,0:-140.222,0,-151.186,-144.436,-155.1,-299.162 1/1:69:0:0:69,0:2506,0:-777.734,-20.7711,0,-777.734,-20.7711,-777.734 0/1:17:10:355:7,0:270,0:-75.5457,0,-107.162,-78.556,-109.269,-187.452 0/1:58:33:1252:25,0:989,0:-271.846,0,-359.488,-281.78,-367.013,-648.405 0/1:35:19:755:16,0:627,0:-174.228,0,-209.735,-179.947,-214.551,-394.104 0/1:26:9:351:17,0:680,0:-189.701,0,-96.1193,-192.41,-101.237,-293.254 0/0:53:53:2059:0,0:0,0:0,-15.9546,-609.511,-15.9546,-609.511,-609.511 0/0:33:32:1269:0,0:0,0:0,-9.63296,-370.162,-9.63296,-370.162,-370.162 0/1:21:12:477:9,0:365,0:-98.8929,0,-132.958,-102.505,-135.668,-237.771 0/1:107:52:1896:55,0:2071,0:-594.399,0,-554.667,-610.053,-571.224,-1180.91 0/1:9:7:281:2,0:50,0:-18.0366,0,-78.9529,-20.1438,-79.555,-99.4154 1/1:22:0:0:22,0:864,0:-254.067,-6.62266,0,-254.067,-6.62266,-254.067 0/1:131:57:2263:72,0:2808,0:-789.722,0,-620.658,-806.881,-642.332,-1449.1 0/0:152:150:5887:1,0:38,0:0,-34.038,-1717.85,-45.1545,-1718.15,-1729.26 0/1:27:14:534:13,0:512,0:-142.297,0,-152.267,-146.511,-156.181,-302.304 . 0/1:7:3:113:4,0:158,0:-44.4921,0,-32.4297,-45.3952,-33.6338,-78.6449 0/0:14:14:544:0,0:0,0:0,-4.21442,-161.298,-4.21442,-161.298,-161.298 0/0:129:127:4963:0,0:0,0:0,-38.2308,-1462.3,-38.2308,-1462.3,-1462.3 0/1:22:13:480:9,0:347,0:-96.9577,0,-140.907,-100.871,-143.616,-244.109 0/0:31:31:1216:0,0:0,0:0,-9.33193,-357.713,-9.33193,-357.713,-357.713
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output1.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,94 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20190323 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig=<ID=Chromosome,length=4411532> +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044" +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out +Chromosome 1849 . C A 3412.24 . AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:0:0:110:3850:-346.644,-33.1133,0.0 +Chromosome 1977 . A G 3234.43 . AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3704:-333.508,-31.9092,0.0 +Chromosome 4013 . T C 3965.91 . AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:125:4448:-400.411,-37.6288,0.0 +Chromosome 11820 . C G 2252.54 . AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:74:0:0:74:2662:-239.791,-22.2762,0.0 +Chromosome 11879 . A G 1815.99 . AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:63:0:0:63:2212:-199.306,-18.9649,0.0 +Chromosome 14785 . T C 4342.4 . AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:139:4874:-438.763,-41.8432,0.0 +Chromosome 14861 . G T 4237.79 . AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:135:0:0:133:4758:-427.969,-40.037,0.0 +Chromosome 15117 . C G 3298.26 . AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3708:-333.903,-31.9092,0.0 +Chromosome 15890 . G A 3349.13 . AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:116:3770:-339.321,-34.9195,0.0 +Chromosome 16119 . C A 3794.09 . AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:124:4268:-383.905,-37.3277,0.0 +Chromosome 21795 . G A 768.571 . AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:28:0:0:28:892:-80.5646,-8.42884,0.0 +Chromosome 25610 . G C 2779.82 . AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3137:-282.515,-26.7917,0.0 +Chromosome 26959 . C G 2791.1 . AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:91:0:0:91:3152:-283.856,-27.3937,0.0 +Chromosome 27455 . T C 1646.76 . AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:52:0:0:52:1868:-168.374,-15.6536,0.0 +Chromosome 28366 . AT A 2447.14 . AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:82:2764:-248.651,-24.6845,0.0 +Chromosome 34044 . T C 3866.76 . AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4351:-391.712,-36.7257,0.0 +Chromosome 36008 . G C 2942.73 . AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:0:0:98:3356:-301.935,-29.5009,0.0 +Chromosome 37031 . C G 3922.6 . AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:129:1:34:128:4437:-396.072,-35.434,0.0 +Chromosome 37305 . C G 4975.87 . AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:5577:-501.976,-47.2617,0.0 +Chromosome 39158 . C G 2017.05 . AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:66:0:0:66:2297:-206.967,-19.868,0.0 +Chromosome 42281 . C A 996.941 . AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:33:0:0:33:1179:-106.407,-9.93399,0.0 +Chromosome 42967 . G C 2851.59 . AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3244:-292.146,-27.6948,0.0 +Chromosome 43347 . T C 2847.24 . AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3233:-291.161,-27.6948,0.0 +Chromosome 44768 . A G 3099.48 . AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:99:3501:-315.241,-29.802,0.0 +Chromosome 49360 . C T 2971.13 . AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:97:0:0:97:3365:-303.059,-29.1999,0.0 +Chromosome 49690 . GCC G 3479.85 . AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:117:3917:-352.709,-35.2205,0.0 +Chromosome 50557 . T C 3743.4 . AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4203:-378.409,-36.4246,0.0 +Chromosome 51949 . A G 3521.52 . AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:112:0:0:112:3955:-356.092,-33.7154,0.0 +Chromosome 54394 . A G 3304.32 . AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:104:3711:-333.937,-31.3071,0.0 +Chromosome 62049 . A G 2249.46 . AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:1:35:77:2659:-236.018,-19.9817,0.0 +Chromosome 63146 . G T 5120.15 . AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:5737:-516.376,-49.0679,0.0 +Chromosome 65150 . C T 4046.85 . AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:134:0:0:134:4538:-408.565,-40.338,0.0 +Chromosome 65246 . C T 3297.8 . AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:107:0:0:106:3712:-334.038,-31.9092,0.0 +Chromosome 68337 . T TC 1791.13 . AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:60:2038:-183.378,-18.0618,0.0 +Chromosome 69989 . G A 3539.46 . AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:119:0:0:119:3973:-357.725,-35.8226,0.0 +Chromosome 70267 . G T 3018.85 . AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:1:25:100:3421:-305.576,-27.9042,0.0 +Chromosome 70816 . A G 4198.57 . AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4707:-423.747,-40.9401,0.0 +Chromosome 71336 . G C 556.161 . AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:21:0:0:21:770:-69.6143,-6.32163,0.0 +Chromosome 71914 . T C 3905.06 . AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4382:-394.523,-37.9298,0.0 +Chromosome 75233 . C A 1903.61 . AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2172:-195.723,-19.2659,0.0 +Chromosome 75940 . G C 2674.83 . AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3048:-274.519,-26.7917,0.0 +Chromosome 87468 . C T 4061.4 . AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4584:-412.628,-37.9298,0.0 +Chromosome 92199 . T G 686.38 . AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:799:-72.2155,-6.92369,0.0 +Chromosome 94388 . G A 2922.87 . AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:95:0:0:95:3292:-296.486,-28.5979,0.0 +Chromosome 99162 . TCGGTGTGCG T 2040.99 . AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2358:-212.453,-23.4803,0.0 +Chromosome 116000 . T G 3196.37 . AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3605:-324.628,-31.6082,0.0 +Chromosome 122109 . A G 3324.29 . AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:111:0:0:111:3735:-336.329,-33.4143,0.0 +Chromosome 123454 . C T 4362.28 . AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:136:4894:-440.321,-40.9401,0.0 +Chromosome 123520 . T C 3793.13 . AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4262:-383.682,-36.4246,0.0 +Chromosome 125711 . GGTT G 3140.7 . AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3531:-317.98,-31.6082,0.0 +Chromosome 125830 . G GA 2079.98 . AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:69:2347:-211.164,-20.7711,0.0 +Chromosome 131174 . T TG 2854.04 . AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:97:3213:-288.972,-29.1999,0.0 +Chromosome 133839 . C T 2457.55 . AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2802:-252.374,-23.4803,0.0 +Chromosome 134024 . T C 2242.53 . AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2543:-229.099,-21.6742,0.0 +Chromosome 138419 . G A 4166.36 . AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:132:0:0:132:4683:-421.582,-39.736,0.0 +Chromosome 139297 . G T 3706.81 . AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:120:0:0:120:4165:-374.978,-36.1236,0.0 +Chromosome 143207 . T C 2180.95 . AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2523:-227.3,-21.6742,0.0 +Chromosome 146087 . T C 4315.28 . AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:137:4844:-436.07,-41.2411,0.0 +Chromosome 147262 . G T 3766.49 . AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4228:-380.649,-36.7257,0.0 +Chromosome 154283 . T C 4403.08 . AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:141:0:0:141:4941:-444.791,-42.4452,0.0 +Chromosome 154990 . G T 4207.92 . AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:143:0:0:142:4724:-424.969,-42.7463,0.0 +Chromosome 162151 . GT G 2208.67 . AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:81:2524:-226.95,-24.3834,0.0 +Chromosome 163940 . A G 2507.97 . AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:80:0:0:80:2839:-255.719,-24.0824,0.0 +Chromosome 166253 . A C 3141.13 . AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:102:0:0:102:3586:-322.902,-30.7051,0.0 +Chromosome 190816 . A C 1715.49 . AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:57:0:0:57:2026:-182.579,-17.1587,0.0 +Chromosome 194305 . C CGG 1602.78 . AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:59:0:0:58:1889:-169.924,-17.4597,0.0 +Chromosome 2738274 . A C 511.15 . AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:19:1:35:18:633:-53.7923,-2.22094,0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output2.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,101 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20190323 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig=<ID=Chromosome,length=4411532> +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044" +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out +Chromosome 1849 . C A 3412.24 . AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:0:0:110:3850:-346.644,-33.1133,0.0 +Chromosome 1977 . A G 3234.43 . AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3704:-333.508,-31.9092,0.0 +Chromosome 4013 . T C 3965.91 . AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:125:4448:-400.411,-37.6288,0.0 +Chromosome 7362 . G C 4009.71 . AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4518:-406.711,-37.9298,0.0 +Chromosome 9304 . G A 4222.23 . AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4764:-428.865,-40.9401,0.0 +Chromosome 11820 . C G 2252.54 . AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:74:0:0:74:2662:-239.791,-22.2762,0.0 +Chromosome 11879 . A G 1815.99 . AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:63:0:0:63:2212:-199.306,-18.9649,0.0 +Chromosome 14785 . T C 4342.4 . AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:139:4874:-438.763,-41.8432,0.0 +Chromosome 14861 . G T 4237.79 . AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:135:0:0:133:4758:-427.969,-40.037,0.0 +Chromosome 15117 . C G 3298.26 . AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3708:-333.903,-31.9092,0.0 +Chromosome 15890 . G A 3349.13 . AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:116:3770:-339.321,-34.9195,0.0 +Chromosome 16119 . C A 3794.09 . AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:124:4268:-383.905,-37.3277,0.0 +Chromosome 21795 . G A 768.571 . AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:28:0:0:28:892:-80.5646,-8.42884,0.0 +Chromosome 25610 . G C 2779.82 . AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3137:-282.515,-26.7917,0.0 +Chromosome 26959 . C G 2791.1 . AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:91:0:0:91:3152:-283.856,-27.3937,0.0 +Chromosome 27455 . T C 1646.76 . AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:52:0:0:52:1868:-168.374,-15.6536,0.0 +Chromosome 28366 . AT A 2447.14 . AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:82:2764:-248.651,-24.6845,0.0 +Chromosome 34044 . T C 3866.76 . AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4351:-391.712,-36.7257,0.0 +Chromosome 36008 . G C 2942.73 . AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:0:0:98:3356:-301.935,-29.5009,0.0 +Chromosome 37031 . C G 3922.6 . AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:129:1:34:128:4437:-396.072,-35.434,0.0 +Chromosome 37305 . C G 4975.87 . AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:5577:-501.976,-47.2617,0.0 +Chromosome 39158 . C G 2017.05 . AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:66:0:0:66:2297:-206.967,-19.868,0.0 +Chromosome 42281 . C A 996.941 . AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:33:0:0:33:1179:-106.407,-9.93399,0.0 +Chromosome 42967 . G C 2851.59 . AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3244:-292.146,-27.6948,0.0 +Chromosome 43347 . T C 2847.24 . AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3233:-291.161,-27.6948,0.0 +Chromosome 44768 . A G 3099.48 . AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:99:3501:-315.241,-29.802,0.0 +Chromosome 49360 . C T 2971.13 . AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:97:0:0:97:3365:-303.059,-29.1999,0.0 +Chromosome 49690 . GCC G 3479.85 . AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:117:3917:-352.709,-35.2205,0.0 +Chromosome 50557 . T C 3743.4 . AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4203:-378.409,-36.4246,0.0 +Chromosome 51949 . A G 3521.52 . AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:112:0:0:112:3955:-356.092,-33.7154,0.0 +Chromosome 54394 . A G 3304.32 . AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:104:3711:-333.937,-31.3071,0.0 +Chromosome 62049 . A G 2249.46 . AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:1:35:77:2659:-236.018,-19.9817,0.0 +Chromosome 63146 . G T 5120.15 . AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:5737:-516.376,-49.0679,0.0 +Chromosome 65150 . C T 4046.85 . AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:134:0:0:134:4538:-408.565,-40.338,0.0 +Chromosome 65246 . C T 3297.8 . AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:107:0:0:106:3712:-334.038,-31.9092,0.0 +Chromosome 68337 . T TC 1791.13 . AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:60:2038:-183.378,-18.0618,0.0 +Chromosome 69989 . G A 3539.46 . AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:119:0:0:119:3973:-357.725,-35.8226,0.0 +Chromosome 70267 . G T 3018.85 . AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:1:25:100:3421:-305.576,-27.9042,0.0 +Chromosome 70816 . A G 4198.57 . AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4707:-423.747,-40.9401,0.0 +Chromosome 71336 . G C 556.161 . AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:21:0:0:21:770:-69.6143,-6.32163,0.0 +Chromosome 71914 . T C 3905.06 . AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4382:-394.523,-37.9298,0.0 +Chromosome 75233 . C A 1903.61 . AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2172:-195.723,-19.2659,0.0 +Chromosome 75940 . G C 2674.83 . AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3048:-274.519,-26.7917,0.0 +Chromosome 87468 . C T 4061.4 . AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4584:-412.628,-37.9298,0.0 +Chromosome 92199 . T G 686.38 . AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:799:-72.2155,-6.92369,0.0 +Chromosome 94388 . G A 2922.87 . AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:95:0:0:95:3292:-296.486,-28.5979,0.0 +Chromosome 99162 . TCGGTGTGCG T 2040.99 . AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2358:-212.453,-23.4803,0.0 +Chromosome 105139 . C A 3418.74 . AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:1:38:109:3888:-346.257,-29.316,0.0 +Chromosome 105736 . T C 1805.18 . AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:61:2101:-189.335,-18.3628,0.0 +Chromosome 116000 . T G 3196.37 . AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3605:-324.628,-31.6082,0.0 +Chromosome 122109 . A G 3324.29 . AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:111:0:0:111:3735:-336.329,-33.4143,0.0 +Chromosome 123454 . C T 4362.28 . AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:136:4894:-440.321,-40.9401,0.0 +Chromosome 123520 . T C 3793.13 . AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4262:-383.682,-36.4246,0.0 +Chromosome 125711 . GGTT G 3140.7 . AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3531:-317.98,-31.6082,0.0 +Chromosome 125830 . G GA 2079.98 . AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:69:2347:-211.164,-20.7711,0.0 +Chromosome 131174 . T TG 2854.04 . AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:97:3213:-288.972,-29.1999,0.0 +Chromosome 133839 . C T 2457.55 . AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2802:-252.374,-23.4803,0.0 +Chromosome 134024 . T C 2242.53 . AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2543:-229.099,-21.6742,0.0 +Chromosome 138419 . G A 4166.36 . AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:132:0:0:132:4683:-421.582,-39.736,0.0 +Chromosome 139297 . G T 3706.81 . AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:120:0:0:120:4165:-374.978,-36.1236,0.0 +Chromosome 143207 . T C 2180.95 . AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2523:-227.3,-21.6742,0.0 +Chromosome 146087 . T C 4315.28 . AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:137:4844:-436.07,-41.2411,0.0 +Chromosome 147262 . G T 3766.49 . AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4228:-380.649,-36.7257,0.0 +Chromosome 154283 . T C 4403.08 . AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:141:0:0:141:4941:-444.791,-42.4452,0.0 +Chromosome 154990 . G T 4207.92 . AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:143:0:0:142:4724:-424.969,-42.7463,0.0 +Chromosome 162151 . GT G 2208.67 . AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:81:2524:-226.95,-24.3834,0.0 +Chromosome 163940 . A G 2507.97 . AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:80:0:0:80:2839:-255.719,-24.0824,0.0 +Chromosome 166253 . A C 3141.13 . AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:102:0:0:102:3586:-322.902,-30.7051,0.0 +Chromosome 177857 . G A 2984.02 . AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:98:0:0:98:3389:-305.192,-29.5009,0.0 +Chromosome 188800 . T C 1887.67 . AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2217:-199.772,-19.2659,0.0 +Chromosome 190816 . A C 1715.49 . AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:57:0:0:57:2026:-182.579,-17.1587,0.0 +Chromosome 194305 . C CGG 1602.78 . AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:59:0:0:58:1889:-169.924,-17.4597,0.0 +Chromosome 2738274 . A C 511.15 . AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:19:1:35:18:633:-53.7923,-2.22094,0.0 +Chromosome 3750185 . CGAC GGTG 1102.73 . AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex GT:DP:RO:QR:AO:QA:GL 1/1:36:0:0:36:1255:-113.24,-10.8371,0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output3.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,101 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20190323 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig=<ID=Chromosome,length=4411532> +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044" +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out +Chromosome 1849 . C A 3412.24 . AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:0:0:110:3850:-346.644,-33.1133,0.0 +Chromosome 1977 . A G 3234.43 . AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3704:-333.508,-31.9092,0.0 +Chromosome 4013 . T C 3965.91 . AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:125:4448:-400.411,-37.6288,0.0 +Chromosome 7362 . G C 4009.71 . AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4518:-406.711,-37.9298,0.0 +Chromosome 9304 . G A 4222.23 . AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4764:-428.865,-40.9401,0.0 +Chromosome 11820 . C G 2252.54 . AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:74:0:0:74:2662:-239.791,-22.2762,0.0 +Chromosome 11879 . A G 1815.99 . AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:63:0:0:63:2212:-199.306,-18.9649,0.0 +Chromosome 14785 . T C 4342.4 . AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:139:4874:-438.763,-41.8432,0.0 +Chromosome 14861 . G T 4237.79 . AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:135:0:0:133:4758:-427.969,-40.037,0.0 +Chromosome 15117 . C G 3298.26 . AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3708:-333.903,-31.9092,0.0 +Chromosome 15890 . G A 3349.13 . AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:116:3770:-339.321,-34.9195,0.0 +Chromosome 16119 . C A 3794.09 . AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:124:4268:-383.905,-37.3277,0.0 +Chromosome 21795 . G A 768.571 . AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:28:0:0:28:892:-80.5646,-8.42884,0.0 +Chromosome 25610 . G C 2779.82 . AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3137:-282.515,-26.7917,0.0 +Chromosome 26959 . C G 2791.1 . AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:91:0:0:91:3152:-283.856,-27.3937,0.0 +Chromosome 27455 . T C 1646.76 . AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:52:0:0:52:1868:-168.374,-15.6536,0.0 +Chromosome 28366 . AT A 2447.14 . AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:82:2764:-248.651,-24.6845,0.0 +Chromosome 34044 . T C 3866.76 . AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4351:-391.712,-36.7257,0.0 +Chromosome 36008 . G C 2942.73 . AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:0:0:98:3356:-301.935,-29.5009,0.0 +Chromosome 37031 . C G 3922.6 . AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:129:1:34:128:4437:-396.072,-35.434,0.0 +Chromosome 37305 . C G 4975.87 . AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:5577:-501.976,-47.2617,0.0 +Chromosome 39158 . C G 2017.05 . AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:66:0:0:66:2297:-206.967,-19.868,0.0 +Chromosome 42281 . C A 996.941 . AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:33:0:0:33:1179:-106.407,-9.93399,0.0 +Chromosome 42967 . G C 2851.59 . AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3244:-292.146,-27.6948,0.0 +Chromosome 43347 . T C 2847.24 . AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3233:-291.161,-27.6948,0.0 +Chromosome 44768 . A G 3099.48 . AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:99:3501:-315.241,-29.802,0.0 +Chromosome 49360 . C T 2971.13 . AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:97:0:0:97:3365:-303.059,-29.1999,0.0 +Chromosome 49690 . GCC G 3479.85 . AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:117:3917:-352.709,-35.2205,0.0 +Chromosome 50557 . T C 3743.4 . AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4203:-378.409,-36.4246,0.0 +Chromosome 51949 . A G 3521.52 . AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:112:0:0:112:3955:-356.092,-33.7154,0.0 +Chromosome 54394 . A G 3304.32 . AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:104:3711:-333.937,-31.3071,0.0 +Chromosome 62049 . A G 2249.46 . AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:1:35:77:2659:-236.018,-19.9817,0.0 +Chromosome 63146 . G T 5120.15 . AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:5737:-516.376,-49.0679,0.0 +Chromosome 65150 . C T 4046.85 . AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:134:0:0:134:4538:-408.565,-40.338,0.0 +Chromosome 65246 . C T 3297.8 . AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:107:0:0:106:3712:-334.038,-31.9092,0.0 +Chromosome 68337 . T TC 1791.13 . AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:60:2038:-183.378,-18.0618,0.0 +Chromosome 69989 . G A 3539.46 . AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:119:0:0:119:3973:-357.725,-35.8226,0.0 +Chromosome 70267 . G T 3018.85 . AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:1:25:100:3421:-305.576,-27.9042,0.0 +Chromosome 70816 . A G 4198.57 . AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4707:-423.747,-40.9401,0.0 +Chromosome 71336 . G C 556.161 . AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:21:0:0:21:770:-69.6143,-6.32163,0.0 +Chromosome 71914 . T C 3905.06 . AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4382:-394.523,-37.9298,0.0 +Chromosome 75233 . C A 1903.61 . AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2172:-195.723,-19.2659,0.0 +Chromosome 75940 . G C 2674.83 . AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3048:-274.519,-26.7917,0.0 +Chromosome 87468 . C T 4061.4 . AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4584:-412.628,-37.9298,0.0 +Chromosome 92199 . T G 686.38 . AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:799:-72.2155,-6.92369,0.0 +Chromosome 94388 . G A 2922.87 . AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:95:0:0:95:3292:-296.486,-28.5979,0.0 +Chromosome 99162 . TCGGTGTGCG T 2040.99 . AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2358:-212.453,-23.4803,0.0 +Chromosome 105139 . C A 3418.74 . AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:1:38:109:3888:-346.257,-29.316,0.0 +Chromosome 105736 . T C 1805.18 . AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:61:2101:-189.335,-18.3628,0.0 +Chromosome 116000 . T G 3196.37 . AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3605:-324.628,-31.6082,0.0 +Chromosome 122109 . A G 3324.29 . AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:111:0:0:111:3735:-336.329,-33.4143,0.0 +Chromosome 123454 . C T 4362.28 . AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:136:4894:-440.321,-40.9401,0.0 +Chromosome 123520 . T C 3793.13 . AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4262:-383.682,-36.4246,0.0 +Chromosome 125711 . GGTT G 3140.7 . AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3531:-317.98,-31.6082,0.0 +Chromosome 125830 . G GA 2079.98 . AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:69:2347:-211.164,-20.7711,0.0 +Chromosome 131174 . T TG 2854.04 . AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:97:3213:-288.972,-29.1999,0.0 +Chromosome 133839 . C T 2457.55 . AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2802:-252.374,-23.4803,0.0 +Chromosome 134024 . T C 2242.53 . AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2543:-229.099,-21.6742,0.0 +Chromosome 138419 . G A 4166.36 . AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:132:0:0:132:4683:-421.582,-39.736,0.0 +Chromosome 139297 . G T 3706.81 . AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:120:0:0:120:4165:-374.978,-36.1236,0.0 +Chromosome 143207 . T C 2180.95 . AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2523:-227.3,-21.6742,0.0 +Chromosome 146087 . T C 4315.28 . AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:137:4844:-436.07,-41.2411,0.0 +Chromosome 147262 . G T 3766.49 . AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4228:-380.649,-36.7257,0.0 +Chromosome 154283 . T C 4403.08 . AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:141:0:0:141:4941:-444.791,-42.4452,0.0 +Chromosome 154990 . G T 4207.92 . AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:143:0:0:142:4724:-424.969,-42.7463,0.0 +Chromosome 162151 . GT G 2208.67 . AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:81:2524:-226.95,-24.3834,0.0 +Chromosome 163940 . A G 2507.97 . AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:80:0:0:80:2839:-255.719,-24.0824,0.0 +Chromosome 166253 . A C 3141.13 . AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:102:0:0:102:3586:-322.902,-30.7051,0.0 +Chromosome 177857 . G A 2984.02 . AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:98:0:0:98:3389:-305.192,-29.5009,0.0 +Chromosome 188800 . T C 1887.67 . AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2217:-199.772,-19.2659,0.0 +Chromosome 190816 . A C 1715.49 . AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:57:0:0:57:2026:-182.579,-17.1587,0.0 +Chromosome 194305 . C CGG 1602.78 . AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:59:0:0:58:1889:-169.924,-17.4597,0.0 +Chromosome 3750185 . CGAC GGTG 1102.73 . AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex GT:DP:RO:QR:AO:QA:GL 1/1:36:0:0:36:1255:-113.24,-10.8371,0.0 +Chromosome 3750193 . G A 1198.75 . AB=0.0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1367:-123.307,-12.0412,0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output4.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,58 @@ +##fileformat=VCFv4.1 +##fileDate=20150301 +##source=freeBayes v0.9.20-16-g3e35e72 +##reference=reference.fasta +##phasing=none +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=technology.Illumina,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from Illumina"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BR_002 BR_004 BR_006 BR_009 BR_013 BR_015 BR_016 BR_021 BR_023 BR_024 BR_025 BR_028 BR_030 BR_031 BR_040 BR_041 BR_043 BR_046 BR_047 BR_048 WL_031 WL_032 WL_054 WL_056 WL_057 WL_058 WL_061 WL_064 WL_066 WL_067 WL_069 WL_070 WL_071 WL_072 WL_076 WL_077 WL_078 WL_079 WL_080 WL_081 +E2_L101 125 . C T 110675 . AB=0.558397;ABP=37.7557;AC=47;AF=0.635135;AN=74;AO=1064;CIGAR=1X;DP=1923;DPB=1923.0;DPRA=0.800123;EPP=2313.46;EPPR=1866.13;GTI=0;LEN=1;MEANALT=1.02941;MQM=60.0;MQMR=60.0;NS=37;NUMALT=1;ODDS=7.31554;PAIRED=1.0;PAIREDR=1.0;PAO=0.0;PQA=0.0;PQR=0.0;PRO=0.0;QA=32732;QR=26625;RO=858;RPL=0.0;RPP=2313.46;RPPR=1866.13;RPR=1064.0;RUN=1;SAF=0;SAP=2313.46;SAR=1064;SRF=0;SRP=1866.13;SRR=858;TYPE=snp;technology.Illumina=1.0 GT:DP:RO:QR:AO:QA:GL 0/1:63:29:919:34:1086:-351.067,0.0,-296.04 0/1:275:136:3998:139:4075:-1396.19,0.0,-1365.26 0/1:17:7:231:10:323:-104.267,0.0,-71.9963 0/0:50:50:1463:0:0:0.0,-15.0515,-531.939 .:.:.:.:.:.:. 0/1:137:73:2205:64:1932:-644.905,0.0,-741.47 0/1:15:6:206:9:301:-94.9006,0.0,-62.3614 0/1:63:14:477:49:1547:-512.541,0.0,-136.291 0/1:5:3:93:2:69:-21.0475,0.0,-31.1725 1/1:13:0:0:13:388:-139.212,-3.91339,0.0 1/1:21:0:0:21:616:-223.722,-6.32163,0.0 0/1:32:7:224:25:787:-261.493,0.0,-66.8418 .:.:.:.:.:.:. 1/1:25:0:0:25:815:-273.654,-7.52575,0.0 0/1:45:23:652:22:616:-218.165,0.0,-229.408 1/1:39:0:0:39:1185:-418.932,-11.7402,0.0 0/1:49:16:469:33:949:-334.932,0.0,-155.746 0/0:14:14:396:0:0:0.0,-4.21442,-147.916 1/1:82:0:0:82:2334:-866.31,-24.6845,0.0 0/1:27:14:431:13:389:-131.174,0.0,-142.961 1/1:68:0:0:68:2019:-725.97,-20.47,0.0 1/1:16:0:0:16:493:-172.669,-4.81648,0.0 0/1:57:2:58:55:1716:-577.549,0.0,-4.35015 1/1:34:0:0:34:1117:-372.828,-10.235,0.0 0/1:25:9:295:16:540:-169.396,0.0,-91.3433 0/1:53:26:837:27:880:-279.548,0.0,-267.677 1/1:33:0:0:33:1063:-359.964,-9.93399,0.0 0/1:21:12:397:9:297:-92.7309,0.0,-125.728 0/1:107:50:1484:57:1738:-580.482,0.0,-501.622 1/1:9:0:0:9:282:-97.6869,-2.70927,0.0 1/1:22:0:0:22:711:-240.294,-6.62266,0.0 0/1:130:57:1814:72:2337:-747.579,0.0,-580.516 0/0:151:150:4800:1:31:0.0,-34.3561,-1621.09 1/1:26:0:0:26:813:-281.46,-7.82678,0.0 .:.:.:.:.:.:. 1/1:7:0:0:7:223:-76.3831,-2.10721,0.0 1/1:13:0:0:13:425:-142.565,-3.91339,0.0 0/0:127:127:4112:0:0:0.0,-38.2308,-1386.3 0/1:21:12:387:9:297:-92.7307,0.0,-124.822 0/1:31:21:677:10:338:-101.416,0.0,-219.904 +E2_L101 189 . GT GA 79493.6 . AB=0.530648;ABP=12.3275;AC=27;AF=0.364865;AN=74;AO=711;CIGAR=1M1X;DP=1947;DPB=1947.0;DPRA=1.2223;EPP=1546.93;EPPR=2623.98;GTI=0;LEN=1;MEANALT=1.2;MQM=59.9536;MQMR=59.9528;NS=37;NUMALT=2;ODDS=8.57375;PAIRED=1.0;PAIREDR=1.0;PAO=0.0;PQA=0.0;PQR=0.0;PRO=0.0;QA=26768;QR=45917;RO=1207;RPL=711.0;RPP=1546.93;RPPR=2623.98;RPR=0.0;RUN=1;SAF=0;SAP=1546.93;SAR=711;SRF=0;SRP=2623.98;SRR=1207;TYPE=snp;technology.Illumina=1.0 GT:DP:RO:QR:AO:QA:GL 0/1:63:29:1128:33,0:1297,0:-362.019,0.0,-314.829,-370.749,-324.763,-695.435 0/1:279:136:5023:143,0:5199,0:-1527.93,0.0,-1456.1,-1568.87,-1499.14,-3067.65 0/0:18:18:720:0,0:0,0:0.0,-5.41854,-209.126,-5.41854,-209.126,-209.126 0/0:50:50:1802:0,0:0,0:0.0,-15.0515,-562.43,-15.0515,-562.43,-562.43 .:.:.:.:.:.:. 0/0:140:140:5188:0,0:0,0:0.0,-42.1442,-1586.93,-42.1442,-1586.93,-1586.93 0/0:15:15:612:0,0:0,0:0.0,-4.51545,-175.417,-4.51545,-175.417,-175.417 0/1:63:14:556:49,0:1902,0:-544.414,0.0,-143.417,-548.629,-158.168,-706.402 0/0:7:7:255:0,0:0,0:0.0,-2.10721,-79.294,-2.10721,-79.294,-79.294 1/1:13:0:0:13,0:486,0:-148.079,-3.91339,0.0,-148.079,-3.91339,-148.079 0/1:21:10:377:11,0:413,0:-119.194,0.0,-107.957,-122.204,-111.268,-233.097 0/1:33:7:283:26,0:969,0:-285.557,0.0,-71.9094,-287.664,-79.7362,-367.003 .:.:.:.:.:.:. 0/1:26:19:720:7,0:270,0:-72.8033,0.0,-209.291,-78.5229,-211.398,-289.538 0/0:45:45:1610:0,0:0,0:0.0,-13.5463,-505.167,-13.5463,-505.167,-505.167 1/2:39:0:0:17,22:633,823:-431.573,-243.764,-238.646,-188.182,0.0,-181.559 0/1:49:16:571:33,0:1209,0:-358.342,0.0,-164.964,-363.158,-174.898,-537.697 0/0:14:14:515:0,0:0,0:0.0,-4.21442,-158.684,-4.21442,-158.684,-158.684 0/1:82:37:1340:45,0:1616,0:-481.016,0.0,-392.198,-492.154,-405.744,-897.538 0/1:27:14:522:13,0:489,0:-140.222,0.0,-151.186,-144.436,-155.1,-299.162 1/1:69:0:0:69,0:2506,0:-777.734,-20.7711,0.0,-777.734,-20.7711,-777.734 0/1:17:10:355:7,0:270,0:-75.5457,0.0,-107.162,-78.556,-109.269,-187.452 0/1:58:33:1252:25,0:989,0:-271.846,0.0,-359.488,-281.78,-367.013,-648.405 0/1:35:19:755:16,0:627,0:-174.228,0.0,-209.735,-179.947,-214.551,-394.104 0/1:26:9:351:17,0:680,0:-189.701,0.0,-96.1193,-192.41,-101.237,-293.254 0/0:53:53:2059:0,0:0,0:0.0,-15.9546,-609.511,-15.9546,-609.511,-609.511 0/0:33:32:1269:0,0:0,0:0.0,-9.63296,-370.162,-9.63296,-370.162,-370.162 0/1:21:12:477:9,0:365,0:-98.8929,0.0,-132.958,-102.505,-135.668,-237.771 0/1:107:52:1896:55,0:2071,0:-594.399,0.0,-554.667,-610.053,-571.224,-1180.91 0/1:9:7:281:2,0:50,0:-18.0366,0.0,-78.9529,-20.1438,-79.555,-99.4154 1/1:22:0:0:22,0:864,0:-254.067,-6.62266,0.0,-254.067,-6.62266,-254.067 0/1:131:57:2263:72,0:2808,0:-789.722,0.0,-620.658,-806.881,-642.332,-1449.1 0/0:152:150:5887:1,0:38,0:0.0,-34.038,-1717.85,-45.1545,-1718.15,-1729.26 0/1:27:14:534:13,0:512,0:-142.297,0.0,-152.267,-146.511,-156.181,-302.304 .:.:.:.:.:.:. 0/1:7:3:113:4,0:158,0:-44.4921,0.0,-32.4297,-45.3952,-33.6338,-78.6449 0/0:14:14:544:0,0:0,0:0.0,-4.21442,-161.298,-4.21442,-161.298,-161.298 0/0:129:127:4963:0,0:0,0:0.0,-38.2308,-1462.3,-38.2308,-1462.3,-1462.3 0/1:22:13:480:9,0:347,0:-96.9577,0.0,-140.907,-100.871,-143.616,-244.109 0/0:31:31:1216:0,0:0,0:0.0,-9.33193,-357.713,-9.33193,-357.713,-357.713
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output5.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,98 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20190323 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig=<ID=Chromosome,length=4411532> +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044" +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out +Chromosome 1849 . C A 3412.24 . AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:0:0:110:3850:-346.644,-33.1133,0.0 +Chromosome 1977 . A G 3234.43 . AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3704:-333.508,-31.9092,0.0 +Chromosome 4013 . T C 3965.91 . AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:125:4448:-400.411,-37.6288,0.0 +Chromosome 7362 . G C 4009.71 . AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4518:-406.711,-37.9298,0.0 +Chromosome 9304 . G A 4222.23 . AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4764:-428.865,-40.9401,0.0 +Chromosome 11820 . C G 2252.54 . AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:74:0:0:74:2662:-239.791,-22.2762,0.0 +Chromosome 11879 . A G 1815.99 . AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:63:0:0:63:2212:-199.306,-18.9649,0.0 +Chromosome 14785 . T C 4342.4 . AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:139:4874:-438.763,-41.8432,0.0 +Chromosome 14861 . G T 4237.79 . AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:135:0:0:133:4758:-427.969,-40.037,0.0 +Chromosome 15117 . C G 3298.26 . AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3708:-333.903,-31.9092,0.0 +Chromosome 15890 . G A 3349.13 . AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:116:3770:-339.321,-34.9195,0.0 +Chromosome 16119 . C A 3794.09 . AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:124:4268:-383.905,-37.3277,0.0 +Chromosome 25610 . G C 2779.82 . AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3137:-282.515,-26.7917,0.0 +Chromosome 26959 . C G 2791.1 . AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:91:0:0:91:3152:-283.856,-27.3937,0.0 +Chromosome 27455 . T C 1646.76 . AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:52:0:0:52:1868:-168.374,-15.6536,0.0 +Chromosome 28366 . AT A 2447.14 . AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:82:2764:-248.651,-24.6845,0.0 +Chromosome 34044 . T C 3866.76 . AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4351:-391.712,-36.7257,0.0 +Chromosome 36008 . G C 2942.73 . AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:0:0:98:3356:-301.935,-29.5009,0.0 +Chromosome 37031 . C G 3922.6 . AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:129:1:34:128:4437:-396.072,-35.434,0.0 +Chromosome 37305 . C G 4975.87 . AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:5577:-501.976,-47.2617,0.0 +Chromosome 39158 . C G 2017.05 . AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:66:0:0:66:2297:-206.967,-19.868,0.0 +Chromosome 42281 . C A 996.941 . AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:33:0:0:33:1179:-106.407,-9.93399,0.0 +Chromosome 42967 . G C 2851.59 . AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3244:-292.146,-27.6948,0.0 +Chromosome 43347 . T C 2847.24 . AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3233:-291.161,-27.6948,0.0 +Chromosome 44768 . A G 3099.48 . AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:99:3501:-315.241,-29.802,0.0 +Chromosome 49360 . C T 2971.13 . AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:97:0:0:97:3365:-303.059,-29.1999,0.0 +Chromosome 49690 . GCC G 3479.85 . AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:117:3917:-352.709,-35.2205,0.0 +Chromosome 50557 . T C 3743.4 . AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4203:-378.409,-36.4246,0.0 +Chromosome 51949 . A G 3521.52 . AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:112:0:0:112:3955:-356.092,-33.7154,0.0 +Chromosome 54394 . A G 3304.32 . AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:104:3711:-333.937,-31.3071,0.0 +Chromosome 62049 . A G 2249.46 . AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:1:35:77:2659:-236.018,-19.9817,0.0 +Chromosome 63146 . G T 5120.15 . AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:5737:-516.376,-49.0679,0.0 +Chromosome 65150 . C T 4046.85 . AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:134:0:0:134:4538:-408.565,-40.338,0.0 +Chromosome 65246 . C T 3297.8 . AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:107:0:0:106:3712:-334.038,-31.9092,0.0 +Chromosome 68337 . T TC 1791.13 . AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:60:2038:-183.378,-18.0618,0.0 +Chromosome 69989 . G A 3539.46 . AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:119:0:0:119:3973:-357.725,-35.8226,0.0 +Chromosome 70267 . G T 3018.85 . AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:1:25:100:3421:-305.576,-27.9042,0.0 +Chromosome 70816 . A G 4198.57 . AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4707:-423.747,-40.9401,0.0 +Chromosome 71914 . T C 3905.06 . AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4382:-394.523,-37.9298,0.0 +Chromosome 75233 . C A 1903.61 . AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2172:-195.723,-19.2659,0.0 +Chromosome 75940 . G C 2674.83 . AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3048:-274.519,-26.7917,0.0 +Chromosome 87468 . C T 4061.4 . AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4584:-412.628,-37.9298,0.0 +Chromosome 94388 . G A 2922.87 . AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:95:0:0:95:3292:-296.486,-28.5979,0.0 +Chromosome 99162 . TCGGTGTGCG T 2040.99 . AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2358:-212.453,-23.4803,0.0 +Chromosome 105139 . C A 3418.74 . AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:1:38:109:3888:-346.257,-29.316,0.0 +Chromosome 105736 . T C 1805.18 . AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:61:2101:-189.335,-18.3628,0.0 +Chromosome 116000 . T G 3196.37 . AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3605:-324.628,-31.6082,0.0 +Chromosome 122109 . A G 3324.29 . AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:111:0:0:111:3735:-336.329,-33.4143,0.0 +Chromosome 123454 . C T 4362.28 . AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:136:4894:-440.321,-40.9401,0.0 +Chromosome 123520 . T C 3793.13 . AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4262:-383.682,-36.4246,0.0 +Chromosome 125711 . GGTT G 3140.7 . AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3531:-317.98,-31.6082,0.0 +Chromosome 125830 . G GA 2079.98 . AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:69:2347:-211.164,-20.7711,0.0 +Chromosome 131174 . T TG 2854.04 . AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:97:3213:-288.972,-29.1999,0.0 +Chromosome 133839 . C T 2457.55 . AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2802:-252.374,-23.4803,0.0 +Chromosome 134024 . T C 2242.53 . AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2543:-229.099,-21.6742,0.0 +Chromosome 138419 . G A 4166.36 . AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:132:0:0:132:4683:-421.582,-39.736,0.0 +Chromosome 139297 . G T 3706.81 . AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:120:0:0:120:4165:-374.978,-36.1236,0.0 +Chromosome 143207 . T C 2180.95 . AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2523:-227.3,-21.6742,0.0 +Chromosome 146087 . T C 4315.28 . AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:137:4844:-436.07,-41.2411,0.0 +Chromosome 147262 . G T 3766.49 . AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4228:-380.649,-36.7257,0.0 +Chromosome 154283 . T C 4403.08 . AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:141:0:0:141:4941:-444.791,-42.4452,0.0 +Chromosome 154990 . G T 4207.92 . AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:143:0:0:142:4724:-424.969,-42.7463,0.0 +Chromosome 162151 . GT G 2208.67 . AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del GT:DP:RO:QR:AO:QA:GL 1/1:84:0:0:81:2524:-226.95,-24.3834,0.0 +Chromosome 163940 . A G 2507.97 . AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:80:0:0:80:2839:-255.719,-24.0824,0.0 +Chromosome 166253 . A C 3141.13 . AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:102:0:0:102:3586:-322.902,-30.7051,0.0 +Chromosome 177857 . G A 2984.02 . AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:98:0:0:98:3389:-305.192,-29.5009,0.0 +Chromosome 188800 . T C 1887.67 . AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2217:-199.772,-19.2659,0.0 +Chromosome 190816 . A C 1715.49 . AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:57:0:0:57:2026:-182.579,-17.1587,0.0 +Chromosome 194305 . C CGG 1602.78 . AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins GT:DP:RO:QR:AO:QA:GL 1/1:59:0:0:58:1889:-169.924,-17.4597,0.0 +Chromosome 3750185 . CGAC GGTG 1102.73 . AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex GT:DP:RO:QR:AO:QA:GL 1/1:36:0:0:36:1255:-113.24,-10.8371,0.0 +Chromosome 3750193 . G A 1198.75 . AB=0.0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1367:-123.307,-12.0412,0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output6.vcf Thu Oct 10 17:59:02 2019 -0400 @@ -0,0 +1,92 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20190323 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig=<ID=Chromosome,length=4411532> +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044" +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out +Chromosome 1849 . C A 3412.24 . AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:0:0:110:3850:-346.644,-33.1133,0.0 +Chromosome 1977 . A G 3234.43 . AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3704:-333.508,-31.9092,0.0 +Chromosome 4013 . T C 3965.91 . AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:125:4448:-400.411,-37.6288,0.0 +Chromosome 7362 . G C 4009.71 . AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4518:-406.711,-37.9298,0.0 +Chromosome 9304 . G A 4222.23 . AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4764:-428.865,-40.9401,0.0 +Chromosome 11820 . C G 2252.54 . AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:74:0:0:74:2662:-239.791,-22.2762,0.0 +Chromosome 11879 . A G 1815.99 . AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:63:0:0:63:2212:-199.306,-18.9649,0.0 +Chromosome 14785 . T C 4342.4 . AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:139:4874:-438.763,-41.8432,0.0 +Chromosome 14861 . G T 4237.79 . AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:135:0:0:133:4758:-427.969,-40.037,0.0 +Chromosome 15117 . C G 3298.26 . AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:106:0:0:106:3708:-333.903,-31.9092,0.0 +Chromosome 15890 . G A 3349.13 . AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:116:3770:-339.321,-34.9195,0.0 +Chromosome 16119 . C A 3794.09 . AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:125:0:0:124:4268:-383.905,-37.3277,0.0 +Chromosome 21795 . G A 768.571 . AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:28:0:0:28:892:-80.5646,-8.42884,0.0 +Chromosome 25610 . G C 2779.82 . AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3137:-282.515,-26.7917,0.0 +Chromosome 26959 . C G 2791.1 . AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:91:0:0:91:3152:-283.856,-27.3937,0.0 +Chromosome 27455 . T C 1646.76 . AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:52:0:0:52:1868:-168.374,-15.6536,0.0 +Chromosome 34044 . T C 3866.76 . AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4351:-391.712,-36.7257,0.0 +Chromosome 36008 . G C 2942.73 . AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:0:0:98:3356:-301.935,-29.5009,0.0 +Chromosome 37031 . C G 3922.6 . AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:129:1:34:128:4437:-396.072,-35.434,0.0 +Chromosome 37305 . C G 4975.87 . AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:5577:-501.976,-47.2617,0.0 +Chromosome 39158 . C G 2017.05 . AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:66:0:0:66:2297:-206.967,-19.868,0.0 +Chromosome 42281 . C A 996.941 . AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:33:0:0:33:1179:-106.407,-9.93399,0.0 +Chromosome 42967 . G C 2851.59 . AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3244:-292.146,-27.6948,0.0 +Chromosome 43347 . T C 2847.24 . AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:92:0:0:92:3233:-291.161,-27.6948,0.0 +Chromosome 44768 . A G 3099.48 . AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:99:0:0:99:3501:-315.241,-29.802,0.0 +Chromosome 49360 . C T 2971.13 . AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:97:0:0:97:3365:-303.059,-29.1999,0.0 +Chromosome 50557 . T C 3743.4 . AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4203:-378.409,-36.4246,0.0 +Chromosome 51949 . A G 3521.52 . AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:112:0:0:112:3955:-356.092,-33.7154,0.0 +Chromosome 54394 . A G 3304.32 . AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:104:3711:-333.937,-31.3071,0.0 +Chromosome 62049 . A G 2249.46 . AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:1:35:77:2659:-236.018,-19.9817,0.0 +Chromosome 63146 . G T 5120.15 . AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:5737:-516.376,-49.0679,0.0 +Chromosome 65150 . C T 4046.85 . AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:134:0:0:134:4538:-408.565,-40.338,0.0 +Chromosome 65246 . C T 3297.8 . AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:107:0:0:106:3712:-334.038,-31.9092,0.0 +Chromosome 69989 . G A 3539.46 . AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:119:0:0:119:3973:-357.725,-35.8226,0.0 +Chromosome 70267 . G T 3018.85 . AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:101:1:25:100:3421:-305.576,-27.9042,0.0 +Chromosome 70816 . A G 4198.57 . AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:136:0:0:136:4707:-423.747,-40.9401,0.0 +Chromosome 71336 . G C 556.161 . AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:21:0:0:21:770:-69.6143,-6.32163,0.0 +Chromosome 71914 . T C 3905.06 . AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4382:-394.523,-37.9298,0.0 +Chromosome 75233 . C A 1903.61 . AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2172:-195.723,-19.2659,0.0 +Chromosome 75940 . G C 2674.83 . AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:89:0:0:89:3048:-274.519,-26.7917,0.0 +Chromosome 87468 . C T 4061.4 . AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:126:0:0:126:4584:-412.628,-37.9298,0.0 +Chromosome 92199 . T G 686.38 . AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:799:-72.2155,-6.92369,0.0 +Chromosome 94388 . G A 2922.87 . AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:95:0:0:95:3292:-296.486,-28.5979,0.0 +Chromosome 105139 . C A 3418.74 . AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:110:1:38:109:3888:-346.257,-29.316,0.0 +Chromosome 105736 . T C 1805.18 . AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:61:0:0:61:2101:-189.335,-18.3628,0.0 +Chromosome 116000 . T G 3196.37 . AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:105:0:0:105:3605:-324.628,-31.6082,0.0 +Chromosome 122109 . A G 3324.29 . AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:111:0:0:111:3735:-336.329,-33.4143,0.0 +Chromosome 123454 . C T 4362.28 . AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:136:4894:-440.321,-40.9401,0.0 +Chromosome 123520 . T C 3793.13 . AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:121:0:0:121:4262:-383.682,-36.4246,0.0 +Chromosome 133839 . C T 2457.55 . AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:78:0:0:78:2802:-252.374,-23.4803,0.0 +Chromosome 134024 . T C 2242.53 . AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2543:-229.099,-21.6742,0.0 +Chromosome 138419 . G A 4166.36 . AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:132:0:0:132:4683:-421.582,-39.736,0.0 +Chromosome 139297 . G T 3706.81 . AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:120:0:0:120:4165:-374.978,-36.1236,0.0 +Chromosome 143207 . T C 2180.95 . AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:72:0:0:72:2523:-227.3,-21.6742,0.0 +Chromosome 146087 . T C 4315.28 . AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:137:0:0:137:4844:-436.07,-41.2411,0.0 +Chromosome 147262 . G T 3766.49 . AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:122:0:0:122:4228:-380.649,-36.7257,0.0 +Chromosome 154283 . T C 4403.08 . AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:141:0:0:141:4941:-444.791,-42.4452,0.0 +Chromosome 154990 . G T 4207.92 . AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:143:0:0:142:4724:-424.969,-42.7463,0.0 +Chromosome 163940 . A G 2507.97 . AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:80:0:0:80:2839:-255.719,-24.0824,0.0 +Chromosome 166253 . A C 3141.13 . AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:102:0:0:102:3586:-322.902,-30.7051,0.0 +Chromosome 177857 . G A 2984.02 . AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:98:0:0:98:3389:-305.192,-29.5009,0.0 +Chromosome 188800 . T C 1887.67 . AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:64:0:0:64:2217:-199.772,-19.2659,0.0 +Chromosome 190816 . A C 1715.49 . AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:57:0:0:57:2026:-182.579,-17.1587,0.0 +Chromosome 2738274 . A C 511.15 . AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:19:1:35:18:633:-53.7923,-2.22094,0.0 +Chromosome 3750193 . G A 1198.75 . AB=0.0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1367:-123.307,-12.0412,0.0