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somatic.Pon.vcf
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somatic.Pon.vcf
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##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --panel-of-normals /workspace/somatico/Mutect2-exome-panel.vcf --germline-resource /workspace/somatico/af-only-gnomad-chr9.vcf.gz --output somatic.Pon.vcf.gz --intervals chr9.interval_list --input tumor_JAK2.bam --reference chr9.fa --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --training-data-mode false --training-data-mode-ref-downsample 2147483647 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.2.2.0",Date="June 8, 2022 at 6:39:50 PM UTC">
##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site">
##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele">
##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele">
##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele">
##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
##MutectVersion=2.2
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives.
##source=Mutect2
##tumor_sample=WP043
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT WP043
9 5026771 . T A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;MBQ=0,20;MFRL=0,128;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=4.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.667:2:0,0:0,1:0,0,1,1
9 5032460 . C A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;MBQ=0,29;MFRL=0,147;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=3.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,1,0
9 5032715 . G T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;MBQ=0,32;MFRL=0,148;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=5.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.667:2:0,0:0,1:0,0,1,1
9 5033052 . G A . . AS_SB_TABLE=0,0|2,1;DP=3;ECNT=1;MBQ=0,20;MFRL=0,87;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=7.70 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,3:0.750:3:0,2:0,0:0,0,2,1
9 5035558 . G A . . AS_SB_TABLE=1,2|0,1;DP=4;ECNT=3;MBQ=20,30;MFRL=110,0;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=3.42 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:3,1:0.400:4:0,1:2,0:0|1:5035558_G_A:5035558:1,2,0,1
9 5035568 . G C . . AS_SB_TABLE=1,2|0,1;DP=4;ECNT=3;MBQ=20,30;MFRL=110,0;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=3.42 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:3,1:0.400:4:0,1:2,0:0|1:5035558_G_A:5035558:1,2,0,1
9 5035578 . C T . . AS_SB_TABLE=1,2|0,1;DP=4;ECNT=3;MBQ=20,27;MFRL=110,0;MMQ=60,60;MPOS=6;POPAF=7.30;TLOD=3.42 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:3,1:0.400:4:0,1:2,0:0|1:5035558_G_A:5035558:1,2,0,1
9 5044364 . C A . . AS_SB_TABLE=211,46|4,2;DP=301;ECNT=1;MBQ=30,20;MFRL=144,95;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=6.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:257,6:0.022:263:87,3:131,1:211,46,4,2
9 5054761 . A G . . AS_SB_TABLE=71,136|4,29;DP=257;ECNT=1;MBQ=30,30;MFRL=163,176;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=76.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:207,33:0.148:240:76,14:100,16:71,136,4,29
9 5064256 . G T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;MBQ=0,20;MFRL=0,68;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=4.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.667:2:0,0:0,1:0,0,1,1
9 5067804 . C A . . AS_SB_TABLE=0,0|2,1;DP=3;ECNT=1;MBQ=0,20;MFRL=0,85;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=7.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,3:0.750:3:0,2:0,0:0,0,2,1
9 5073681 . C CT . . AS_SB_TABLE=74,19|5,1;DP=106;ECNT=2;MBQ=31,31;MFRL=157,165;MMQ=60,60;MPOS=19;POPAF=7.30;RPA=10,11;RU=T;STR;TLOD=3.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:93,6:0.063:99:28,2:47,3:74,19,5,1
9 5073770 . G T . . AS_SB_TABLE=35,95|5,30;DP=171;ECNT=2;MBQ=29,29;MFRL=127,159;MMQ=60,60;MPOS=17;POPAF=3.40;TLOD=82.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:130,35:0.241:165:12,3:25,4:35,95,5,30
9 5076360 . T C . . AS_SB_TABLE=0,0|0,0;DP=6;ECNT=1;MBQ=0,31;MFRL=0,76;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=6.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.764:2:0,2:0,0:0,0,2,0
9 5082218 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;MBQ=0,29;MFRL=0,106;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=3.01 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.684:1:0,1:0,0:0,0,0,1
9 5101126 . G T . . AS_SB_TABLE=1,1|1,1;DP=4;ECNT=1;MBQ=31,20;MFRL=144,78;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=3.87 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:2,2:0.400:4:2,0:0,1:1,1,1,1
9 5101271 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;MBQ=0,30;MFRL=0,150;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=3.18 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,1,0
9 5111548 . T TG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;MBQ=0,30;MFRL=0,72;MMQ=60,60;MPOS=6;POPAF=7.30;TLOD=3.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,1:0,0:0,0,1,0
9 5113796 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=2;MBQ=0,20;MFRL=0,109;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=4.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.667:2:0,0:0,1:0,0,1,1
9 5113937 . C A . . AS_SB_TABLE=1,0|1,1;DP=3;ECNT=2;MBQ=32,20;MFRL=189,58;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=4.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,2:0.500:3:0,1:1,0:1,0,1,1
9 5116138 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;MBQ=0,20;MFRL=0,61;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=4.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.667:2:0,1:0,0:0,0,1,1
9 5122910 . GT G . . AS_SB_TABLE=14,1|3,0;DP=19;ECNT=1;MBQ=30,33;MFRL=211,258;MMQ=60,60;MPOS=37;POPAF=7.30;RPA=11,10;RU=T;STR;TLOD=3.28 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:15,3:0.209:18:8,1:6,2:14,1,3,0