##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=FAD,Number=R,Type=Integer,Description="Count of fragments 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 --tumor-sample NA12891 --output output.vcf --input tumor.bam --input normal.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --base-qual-correction-factor 5 --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 --flow-mode NONE --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 --likelihood-calculation-engine PairHMM --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 --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --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 --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="4.6.2.0",Date="February 2, 2026, 12:30:34?AM GMT">
##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 potential somatic events in the assembly region">
##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele">
##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="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=chr20,length=63025520>
##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##source=Mutect2
##tumor_sample=NA12891
##tumor_sample=NA12892
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
chr20	862991	.	C	G	.	.	AS_SB_TABLE=10,7|4,1;DP=22;ECNT=1;ECNTH=1;MBQ=39,37;MFRL=340,366;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=11.91	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:5,5:0.491:10:4,3:1,1:5,5:1,4,4,1	0/1:12,0:0.071:12:6,0:6,0:12,0:9,3,0,0
chr20	863148	.	C	CTAT	.	.	AS_SB_TABLE=19,18|4,5;DP=49;ECNT=1;ECNTH=1;MBQ=38,39;MFRL=351,362;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=1,2;RU=TAT;STR;TLOD=29.76	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:11,9:0.454:20:4,4:6,4:11,9:5,6,4,5	0/1:26,0:0.034:26:14,0:11,0:26,0:14,12,0,0
chr20	863271	.	A	G	.	.	AS_SB_TABLE=25,9|6,4;DP=45;ECNT=1;ECNTH=1;MBQ=36,37;MFRL=347,361;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=28.96	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:8,10:0.550:18:4,5:4,5:8,10:7,1,6,4	0/1:26,0:0.035:26:16,0:10,0:26,0:18,8,0,0
chr20	863508	.	A	G	.	.	AS_SB_TABLE=24,24|6,6;DP=63;ECNT=1;ECNTH=1;MBQ=39,40;MFRL=342,355;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=36.39	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:11,12:0.524:23:6,6:4,6:11,12:4,7,6,6	0/1:37,0:0.025:37:17,0:17,0:37,0:20,17,0,0
chr20	863706	.	C	T	.	.	AS_SB_TABLE=7,25|8,11;DP=52;ECNT=2;ECNTH=2;MBQ=37,39;MFRL=341,347;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=65.15	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,19:0.953:19:0,12:0,7:0,19:0,0,8,11	0/1:32,0:0.029:32:9,0:23,0:32,0:7,25,0,0
chr20	863744	.	C	T	.	.	AS_SB_TABLE=10,24|6,6;DP=48;ECNT=2;ECNTH=2;MBQ=39,38;MFRL=341,347;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=38.56	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:8,12:0.591:20:5,7:3,5:8,12:4,4,6,6	0/1:26,0:0.035:26:10,0:16,0:26,0:6,20,0,0
chr20	863846	.	C	T	.	.	AS_SB_TABLE=27,10|5,3;DP=47;ECNT=2;ECNTH=1;MBQ=40,37;MFRL=347,348;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=23.22	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:16,8:0.346:24:11,6:5,2:16,8:13,3,5,3	0/1:21,0:0.043:21:9,0:12,0:21,0:14,7,0,0
chr20	863873	.	C	T	.	.	AS_SB_TABLE=23,11|7,3;DP=47;ECNT=2;ECNTH=1;MBQ=39,37;MFRL=353,337;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=30.16	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:21,0:0.042:21:14,0:6,0:21,0:15,6,0,0	0/1:13,10:0.440:23:8,3:5,7:13,10:8,5,7,3
chr20	864074	.	T	C	.	.	AS_SB_TABLE=19,21|8,3;DP=54;ECNT=1;ECNTH=1;MBQ=38,36;MFRL=345,355;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=31.87	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:14,11:0.447:25:7,9:6,2:14,11:5,9,8,3	0/1:26,0:0.035:26:13,0:13,0:26,0:14,12,0,0
chr20	864199	.	G	A	.	.	AS_SB_TABLE=30,18|4,9;DP=63;ECNT=1;ECNTH=1;MBQ=36,39;MFRL=343,361;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=37.97	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:15,13:0.470:28:7,7:7,6:15,13:13,2,4,9	0/1:33,0:0.028:33:23,0:10,0:33,0:17,16,0,0
chr20	864301	.	G	T	.	.	AS_SB_TABLE=20,17|12,6;DP=57;ECNT=1;ECNTH=1;MBQ=35,35;MFRL=344,358;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=56.37	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:12,18:0.594:30:9,12:3,6:12,18:6,6,12,6	0/1:25,0:0.036:25:11,0:14,0:25,0:14,11,0,0
chr20	864455	.	T	C	.	.	AS_SB_TABLE=11,17|15,17;DP=63;ECNT=2;ECNTH=2;MBQ=35,39;MFRL=343,360;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=115.14	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,32:0.971:32:0,16:0,16:0,32:0,0,15,17	0/1:28,0:0.033:28:19,0:8,0:28,0:11,17,0,0
chr20	864512	.	A	G	.	.	AS_SB_TABLE=17,22|11,15;DP=71;ECNT=2;ECNTH=2;MBQ=38,37;MFRL=344,364;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=88.07	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:14,26:0.647:40:8,12:5,14:14,26:9,5,11,15	0/1:25,0:0.035:25:12,0:12,0:25,0:8,17,0,0
chr20	864640	.	C	T	.	.	AS_SB_TABLE=17,18|14,14;DP=65;ECNT=2;ECNTH=2;MBQ=37,35;MFRL=339,354;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=94.52	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,28:0.968:28:0,11:0,17:0,28:0,0,14,14	0/1:35,0:0.027:35:23,0:12,0:35,0:17,18,0,0
chr20	864660	.	G	T	.	.	AS_SB_TABLE=15,15|11,11;DP=54;ECNT=2;ECNTH=2;MBQ=37,38;MFRL=341,358;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=69.93	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,22:0.960:22:0,8:0,12:0,22:0,0,11,11	0/1:30,0:0.031:30:17,0:13,0:30,0:15,15,0,0
chr20	865054	.	G	C	.	.	AS_SB_TABLE=10,9|6,4;DP=31;ECNT=1;ECNTH=1;MBQ=35,34;MFRL=347,347;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=29.95	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:10,10:0.500:20:8,6:2,4:10,10:6,4,6,4	0/1:9,0:0.092:9:3,0:5,0:9,0:4,5,0,0
chr20	865366	.	G	T	.	.	AS_SB_TABLE=13,13|15,11;DP=54;ECNT=1;ECNTH=1;MBQ=39,37;MFRL=343,353;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=88.44	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,26:0.965:26:0,14:0,10:0,26:0,0,15,11	0/1:26,0:0.035:26:10,0:16,0:26,0:13,13,0,0
chr20	865537	.	C	T	.	.	AS_SB_TABLE=17,30|6,5;DP=61;ECNT=1;ECNTH=1;MBQ=35,35;MFRL=350,358;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=28.19	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:20,11:0.358:31:10,5:10,5:20,11:8,12,6,5	0/1:27,0:0.034:27:13,0:13,0:27,0:9,18,0,0
chr20	865664	.	TC	T	.	.	AS_SB_TABLE=20,21|9,11;DP=63;ECNT=1;ECNTH=1;MBQ=35,35;MFRL=347,359;MMQ=60,60;MPOS=23;POPAF=7.30;RPA=4,3;RU=C;STR;TLOD=51.28	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:19,20:0.512:39:10,12:9,5:19,20:11,8,9,11	0/1:22,0:0.042:22:7,0:10,0:22,0:9,13,0,0