##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##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 M12_233TTGLT3_ACCGGAGT-AAGGAAGG --panel-of-normals /data/gpfs/projects/punim2311/reference/1000g_pon.hg38.vcf.gz --germline-resource /data/gpfs/projects/punim2311/reference/af-only-gnomad.hg38.vcf.gz --output /data/gpfs/projects/punim2311/Lorey_mutation_data/output/vcfs/M12_233TTGLT3_ACCGGAGT-AAGGAAGG_unflt.vcf.gz --input /data/gpfs/projects/punim2311/Lorey_mutation_data/output/recal_bams/M12_233TTGLT3_ACCGGAGT-AAGGAAGG_recal.bam --reference /data/gpfs/projects/punim2311/reference/Human_genecode47/GRCh38.fa --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --flow-use-t0-tag false --flow-probability-threshold 0.003 --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 --flow-number-of-uncertain-flows-to-clip 0 --flow-nucleotide-of-first-uncertain-flow T --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --mutect3-training-mode false --mutect3-ref-downsample 10 --mutect3-alt-downsample 20 --mutect3-non-artifact-ratio 20 --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 --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 --pileup-detection-enable-indel-pileup-calling false --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 0.5 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --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 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman JAVA --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 --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="4.3.0.0",Date="3 September 2025 at 8:58:44 pm AEST">
##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=chr7,length=159345973>
##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##source=Mutect2
##tumor_sample=M12_233TTGLT3_ACCGGAGT-AAGGAAGG
##bcftools_normVersion=1.15.1+htslib-1.15.1
##bcftools_normCommand=norm -m -any -f /data/gpfs/projects/punim2311/reference/Human_genecode47/GRCh38.fa ./vcfs/M12_233TTGLT3_ACCGGAGT-AAGGAAGG_unflt.vcf.gz; Date=Mon Dec 15 13:58:46 2025
##bcftools_viewVersion=1.15.1+htslib-1.15.1
##bcftools_viewCommand=view -v snps -Oz -o ./SNVS/M12_233TTGLT3_ACCGGAGT-AAGGAAGG_snv_vcf.gz; Date=Mon Dec 15 13:58:46 2025
##bcftools_mergeVersion=1.15.1+htslib-1.15.1
##bcftools_mergeCommand=merge -Oz -o combined_all_samples.vcf.gz M12_233TTGLT3_ACCGGAGT-AAGGAAGG_snv_vcf.gz M19_233TTGLT3_CAACCGAG-TACCTGTG_snv_vcf.gz M2_233TTGLT3_TCAGCGCC-ATGTTCCT_snv_vcf.gz M5_233TTGLT3_TTGCGTTA-TTCCCGAA_snv_vcf.gz M14_233TTGLT3_CTTGACGA-GCACACAA_snv_vcf.gz M20_233TTGLT3_ACAAGGCA-TCGCGCAA_snv_vcf.gz M30_233TTGLT3_TGTTCGCC-AGGTAGGA_snv_vcf.gz M16_233TTGLT3_CCTATGCA-GAGTCGAT_snv_vcf.gz M22_233TTGLT3_TCTGGAAC-TAGCACCT_snv_vcf.gz M4_233TTGLT3_CACTAGAC-TGAGGACT_snv_vcf.gz; Date=Mon Dec 22 13:20:39 2025
##bcftools_viewVersion=1.13+htslib-1.20-64-g8e3ef4b9
##bcftools_viewCommand=view -R high_quality_considered_mutations_sorted_drm.tsv -o high_quality_considered_mutations_sorted.vcf combined_all_samples.vcf.gz; Date=Mon Jan 12 11:24:55 2026
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	M12_233TTGLT3_ACCGGAGT-AAGGAAGG	M19_233TTGLT3_CAACCGAG-TACCTGTG	M2_233TTGLT3_TCAGCGCC-ATGTTCCT	M5_233TTGLT3_TTGCGTTA-TTCCCGAA	M14_233TTGLT3_CTTGACGA-GCACACAA	M20_233TTGLT3_ACAAGGCA-TCGCGCAA	M30_233TTGLT3_TGTTCGCC-AGGTAGGA	M16_233TTGLT3_CCTATGCA-GAGTCGAT	M22_233TTGLT3_TCTGGAAC-TAGCACCT	M4_233TTGLT3_CACTAGAC-TGAGGACT
chr7	140753336	.	A	T	.	.	AS_SB_TABLE=1,4|24,18;ECNT=5;DP=394;MBQ=20,30;MFRL=118,188;MMQ=60,60;MPOS=32;POPAF=7.3;TLOD=63.55	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:5,42:0.849:47:2,10:2,15:4,27:1,4,24,18	0/1:7,42:0.818:49:0,11:5,11:5,26:4,3,21,21	0/0/1:11,25:0.554:38:6,2:3,10:9,15:4,7,11,16	0/0/1:13,17:0.414:34:7,3:2,5:10,10:3,10,7,14	0/1:5,25:0.81:30:1,4:2,11:3,16:3,2,14,11	0/1:1,22:0.896:23:1,7:0,4:1,16:0,1,10,12	0/1:5,42:0.845:47:2,17:2,6:4,26:3,2,21,21	0/1:8,35:0.793:43:2,10:1,11:5,22:4,4,19,16	0/1:11,40:0.758:51:3,10:3,10:7,24:6,5,17,23	0/0/1:4,21:0.785:27:0,4:1,9:1,16:3,1,12,11