Mercurial > repos > trinity_ctat > ctat_mutations
view test-data/varcalling.outdir/cancer.vcf @ 0:d4a8f440a518 draft
Adding ctat_mutations tool.
| author | trinity_ctat |
|---|---|
| date | Tue, 30 Oct 2018 12:28:26 -0400 |
| parents | |
| children |
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##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##FILTER=<ID=FS,Description="FS > 30.0"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=QD,Description="QD < 2.0"> ##FILTER=<ID=SnpCluster,Description="SNPs found in clusters"> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --input /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --emit-ref-confidence NONE --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations 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 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --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 --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 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.10.0,Date="October 29, 2018 1:03:15 PM EDT"> ##GATKCommandLine=<ID=VariantFiltration,CommandLine="VariantFiltration --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants_initial_filtering.vcf --filter-expression FS > 30.0 --filter-expression QD < 2.0 --filter-name FS --filter-name QD --cluster-size 3 --cluster-window-size 35 --variant /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --mask-extension 0 --mask-name Mask --filter-not-in-mask false --missing-values-evaluate-as-failing false --invalidate-previous-filters false --invert-filter-expression false --invert-genotype-filter-expression false --set-filtered-genotype-to-no-call 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 --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",Version=4.0.10.0,Date="October 29, 2018 1:15:13 PM EDT"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele in the same order as listed"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency for each ALT allele in the same order as listed"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC) for each ALT allele in the same order as listed"> ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF) for each ALT allele in the same order as listed"> ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> ##contig=<ID=chr1,length=248956422> ##contig=<ID=chr2,length=242193529> ##contig=<ID=chr3,length=198295559> ##contig=<ID=chr4,length=190214555> ##contig=<ID=chr5,length=181538259> ##contig=<ID=chr6,length=170805979> ##contig=<ID=chr7,length=159345973> ##contig=<ID=chr8,length=145138636> ##contig=<ID=chr9,length=138394717> ##contig=<ID=chr10,length=133797422> ##contig=<ID=chr11,length=135086622> ##contig=<ID=chr12,length=133275309> ##contig=<ID=chr13,length=114364328> ##contig=<ID=chr14,length=107043718> ##contig=<ID=chr15,length=101991189> ##contig=<ID=chr16,length=90338345> ##contig=<ID=chr17,length=83257441> ##contig=<ID=chr18,length=80373285> ##contig=<ID=chr19,length=58617616> ##contig=<ID=chr20,length=64444167> ##contig=<ID=chr21,length=46709983> ##contig=<ID=chr22,length=50818468> ##contig=<ID=chrX,length=156040895> ##contig=<ID=chrY,length=57227415> ##contig=<ID=chrM,length=16569> ##source=HaplotypeCaller ##source=VariantFiltration ##SnpEffVersion="4.1k (build 2015-09-07), by Pablo Cingolani" ##SnpEffCmd="SnpEff -nostats -noLof -no-downstream -no-upstream hg38 " ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> ##INFO=<ID=GENE,Number=.,Type=String,Description="The name of the gene/s in the genomic region of the SNP as annotated by SNPeff"> ##INFO=<ID=COSMIC_ID,Number=.,Type=String,Description="COSMIC mutation id (unique)."> ##INFO=<ID=TISSUE,Number=.,Type=String,Description="The primary tissue/cancer and subtype from which the sample originated."> ##INFO=<ID=TUMOR,Number=.,Type=String,Description="The histological classification of the sample."> ##INFO=<ID=FATHMM,Number=.,Type=String,Description="FATHMM (Functional Analysis through Hidden Markov Models). 'Pathogenic':Cancer or damaging 'Neutral':Passanger or Tolerated."> ##INFO=<ID=SOMATIC,Number=.,Type=String,Description="Information on whether the sample was reported to be Confirmed Somatic. 'Confirmed somatic':if the mutation has been confimed to be somatic in the experiment by sequencing both the tumour and a matched normal from the same patient 'Previously Observed':when the mutation has been reported as somatic previously but not in current paper 'variant of unknown origin':when the mutation is known to be somatic but the tumour was sequenced without a matched normal"> ##bcftools_annotateVersion=1.9+htslib-1.9 ##bcftools_annotateCommand=annotate --output-type z --annotations /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/cosmic.vcf.gz --columns INFO/COSMIC_ID,INFO/TISSUE,INFO/TUMOR,INFO/FATHMM,INFO/SOMATIC --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_annotated.vcf.gz /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz; Date=Mon Oct 29 13:22:17 2018 ##INFO=<ID=CHASM_PVALUE,Number=.,Type=Float,Description="CHASM cancer driver p-value (missense) generated by CRAVAT"> ##INFO=<ID=CHASM_FDR,Number=.,Type=Float,Description="CHASM cancer driver FDR (missense)"> ##INFO=<ID=VEST_PVALUE,Number=.,Type=Float,Description="VEST pathogenicity p-value (non-silent)"> ##INFO=<ID=VEST_FDR,Number=.,Type=Float,Description="VEST pathogenicity FDR (non-silent)"> ##bcftools_annotateCommand=annotate --annotations /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/Variant_result_updated.tsv.gz -h /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/header/cravat_annotation.txt --columns CHROM,POS,CHASM_PVALUE,CHASM_FDR,VEST_PVALUE,VEST_FDR --output-type z --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_initial_filtering_clean_snp_RNAedit_cosmic_filtered_cravat_annotated_coding.vcf.gz /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_initial_filtering_clean_snp_RNAedit_cosmic_filtered.vcf; Date=Mon Oct 29 13:23:53 2018 ##bcftools_annotateCommand=annotate --annotations /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/Variant_non_coding_result_updated.tsv.gz -h /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/header/cravat_annotation.txt --columns CHROM,POS,CHASM_PVALUE,CHASM_FDR,VEST_PVALUE,VEST_FDR --output-type z --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/annotated_min_filtered.vcf.gz /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/variants_initial_filtering_clean_snp_RNAedit_cosmic_filtered_cravat_annotated_coding.vcf.gz; Date=Mon Oct 29 13:23:53 2018 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_1_fastq chr5 474989 . A G 96.03 PASS GENE=LOC100288152,SLC9A3;AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=24.01;SOR=1.609;ANN=G|missense_variant|MODERATE|SLC9A3|SLC9A3|transcript|NM_004174.2|Coding|16/17|c.2395T>C|p.Cys799Arg|2507/2777|2395/2505|799/834||,G|missense_variant|MODERATE|SLC9A3|SLC9A3|transcript|NM_001284351.1|Coding|16/17|c.2368T>C|p.Cys790Arg|2480/2750|2368/2478|790/825||,G|intron_variant|MODIFIER|LOC100288152|LOC100288152|transcript|NR_125375.1|Noncoding|1/6|n.165-148A>G||||||;COSMIC_ID=COSM4006021;TISSUE=urinary_tract;TUMOR=carcinoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.1114;CHASM_FDR=0.2;VEST_PVALUE=0.96802;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:124,12,0 chr5 181224474 . G A 349.77 PASS GENE=TRIM41;AC=1;AF=0.5;AN=2;BaseQRankSum=0.32;DP=45;ExcessHet=3.0103;FS=1.237;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=7.77;ReadPosRankSum=0.504;SOR=0.945;ANN=A|missense_variant|MODERATE|TRIM41|TRIM41|transcript|NM_033549.4|Coding|1/6|c.475G>A|p.Glu159Lys|1212/3663|475/1893|159/630||,A|missense_variant|MODERATE|TRIM41|TRIM41|transcript|NM_201627.2|Coding|1/8|c.475G>A|p.Glu159Lys|1212/2723|475/1557|159/518||,A|non_coding_exon_variant|MODIFIER|TRIM41|TRIM41|transcript|NR_045218.1|Noncoding|1/7|n.1212G>A||||||;CHASM_PVALUE=0.0694;CHASM_FDR=0.15;VEST_PVALUE=0.48052;VEST_FDR=1 GT:AD:DP:GQ:PL 0/1:28,17:45:99:378,0,717 chr8 143923759 . G A 838.77 PASS GENE=PLEC;AC=1;AF=0.5;AN=2;BaseQRankSum=-0.63;DP=66;ExcessHet=3.0103;FS=0.94;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=12.71;ReadPosRankSum=0.567;SOR=0.82;ANN=A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201380.3|Coding|31/32|c.6581C>T|p.Ala2194Val|6751/15255|6581/14055|2194/4684||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201384.2|Coding|31/32|c.6170C>T|p.Ala2057Val|6299/14803|6170/13644|2057/4547||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201383.2|Coding|31/32|c.6182C>T|p.Ala2061Val|6191/14695|6182/13656|2061/4551||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201382.3|Coding|31/32|c.6170C>T|p.Ala2057Val|6238/14742|6170/13644|2057/4547||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201381.2|Coding|31/32|c.6074C>T|p.Ala2025Val|6148/14652|6074/13548|2025/4515||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201379.2|Coding|31/32|c.6104C>T|p.Ala2035Val|6253/14757|6104/13578|2035/4525||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_201378.3|Coding|31/32|c.6128C>T|p.Ala2043Val|6185/14689|6128/13602|2043/4533||,A|missense_variant|MODERATE|PLEC|PLEC|transcript|NM_000445.4|Coding|32/33|c.6251C>T|p.Ala2084Val|6300/14804|6251/13725|2084/4574||;COSMIC_ID=COSM3750086;TISSUE=large_intestine;TUMOR=carcinoma_--_adenocarcinoma;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0344;CHASM_FDR=0.1;VEST_PVALUE=0.84202;VEST_FDR=1 GT:AD:DP:GQ:PL 0/1:31,35:66:99:867,0,736 chr12 56420869 . G A 384.77 PASS GENE=TIMELESS;AC=1;AF=0.5;AN=2;BaseQRankSum=2.348;DP=48;ExcessHet=3.0103;FS=4.262;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=8.02;ReadPosRankSum=0.096;SOR=0.674;ANN=A|missense_variant|MODERATE|TIMELESS|TIMELESS|transcript|NM_003920.3|Coding|25/29|c.3053C>T|p.Pro1018Leu|3221/5138|3053/3627|1018/1208||;COSMIC_ID=COSM3753397;TISSUE=large_intestine;TUMOR=carcinoma_--_adenocarcinoma;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0744;CHASM_FDR=0.15;VEST_PVALUE=0.18439;VEST_FDR=0.95 GT:AD:DP:GQ:PL 0/1:30,18:48:99:413,0,759 chr17 7673767 . C T 1848.77 PASS GENE=TP53;AC=2;AF=1;AN=2;DP=61;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=30.31;SOR=1.609;ANN=T|missense_variant|MODERATE|TP53|TP53|transcript|NM_000546.5|Coding|8/11|c.853G>A|p.Glu285Lys|1055/2591|853/1182|285/393||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126115.1|Coding|4/7|c.457G>A|p.Glu153Lys|735/2271|457/786|153/261||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126116.1|Coding|4/8|c.457G>A|p.Glu153Lys|735/2404|457/630|153/209||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126117.1|Coding|4/8|c.457G>A|p.Glu153Lys|735/2331|457/645|153/214||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276697.1|Coding|4/7|c.376G>A|p.Glu126Lys|735/2271|376/705|126/234||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276698.1|Coding|4/8|c.376G>A|p.Glu126Lys|735/2404|376/549|126/182||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276699.1|Coding|4/8|c.376G>A|p.Glu126Lys|735/2331|376/564|126/187||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126112.2|Coding|8/11|c.853G>A|p.Glu285Lys|1052/2588|853/1182|285/393||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126113.2|Coding|8/12|c.853G>A|p.Glu285Lys|1055/2651|853/1041|285/346||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126114.2|Coding|8/12|c.853G>A|p.Glu285Lys|1055/2724|853/1026|285/341||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126118.1|Coding|7/10|c.736G>A|p.Glu246Lys|1172/2708|736/1065|246/354||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276695.1|Coding|8/12|c.736G>A|p.Glu246Lys|1055/2651|736/924|246/307||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276696.1|Coding|8/12|c.736G>A|p.Glu246Lys|1055/2724|736/909|246/302||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276760.1|Coding|8/11|c.736G>A|p.Glu246Lys|1055/2591|736/1065|246/354||,T|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276761.1|Coding|8/11|c.736G>A|p.Glu246Lys|1052/2588|736/1065|246/354||;COSMIC_ID=COSM3717625;TISSUE=bone;TUMOR=Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0;CHASM_FDR=0.05;VEST_PVALUE=0.01447;VEST_FDR=0.15 GT:AD:DP:GQ:PL 1/1:0,61:61:99:1877,183,0 chr17 7676154 . G C 2161.77 PASS GENE=TP53;AC=2;AF=1;AN=2;BaseQRankSum=3.225;DP=80;ExcessHet=3.0103;FS=14.289;MLEAC=2;MLEAF=1;MQ=60;MQRankSum=0;QD=27.02;ReadPosRankSum=-2.023;SOR=0.642;ANN=C|missense_variant|MODERATE|TP53|TP53|transcript|NM_000546.5|Coding|4/11|c.215C>G|p.Pro72Arg|417/2591|215/1182|72/393||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126112.2|Coding|4/11|c.215C>G|p.Pro72Arg|414/2588|215/1182|72/393||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126113.2|Coding|4/12|c.215C>G|p.Pro72Arg|417/2651|215/1041|72/346||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126114.2|Coding|4/12|c.215C>G|p.Pro72Arg|417/2724|215/1026|72/341||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001126118.1|Coding|3/10|c.98C>G|p.Pro33Arg|534/2708|98/1065|33/354||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276695.1|Coding|4/12|c.98C>G|p.Pro33Arg|417/2651|98/924|33/307||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276696.1|Coding|4/12|c.98C>G|p.Pro33Arg|417/2724|98/909|33/302||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276760.1|Coding|4/11|c.98C>G|p.Pro33Arg|417/2591|98/1065|33/354||,C|missense_variant|MODERATE|TP53|TP53|transcript|NM_001276761.1|Coding|4/11|c.98C>G|p.Pro33Arg|414/2588|98/1065|33/354||;COSMIC_ID=COSM3766193;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Reported_in_another_cancer_sample_as_somatic;CHASM_PVALUE=0.087;CHASM_FDR=0.15;VEST_PVALUE=0.52717;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:4,76:80:99:2190,183,0 chr17 43071077 . T C 92.03 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=23.01;SOR=3.258;ANN=C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|16/24|c.4900A>G|p.Ser1634Gly|5132/7270|4900/5655|1634/1884||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007298.3|Coding|14/22|c.1525A>G|p.Ser509Gly|1544/3682|1525/2280|509/759||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|14/22|c.4696A>G|p.Ser1566Gly|4977/7115|4696/5451|1566/1816||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007299.3|Coding|15/22|c.1525A>G|p.Ser509Gly|1719/3783|1525/2100|509/699||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|15/23|c.4837A>G|p.Ser1613Gly|5069/7207|4837/5592|1613/1863||,C|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|15/23|n.4973A>G||||||;COSMIC_ID=COSM3755560;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0372;CHASM_FDR=0.1;VEST_PVALUE=0.3446;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:120,12,0 chr17 43091983 . T C 84.03 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=21.01;SOR=0.693;ANN=C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.3548A>G|p.Lys1183Arg|3780/7270|3548/5655|1183/1884||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.3407A>G|p.Lys1136Arg|3688/7115|3407/5451|1136/1816||,C|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.3548A>G|p.Lys1183Arg|3780/7207|3548/5592|1183/1863||,C|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.788-951A>G||||||,C|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.788-951A>G||||||,C|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.3684A>G||||||;COSMIC_ID=COSM3755561;TISSUE=soft_tissue;TUMOR=haemangioblastoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0002;CHASM_FDR=0.05;VEST_PVALUE=0.64447;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:112,12,0 chr17 43092919 . G A 33.74 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=2;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=16.87;SOR=2.303;ANN=A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2612C>T|p.Pro871Leu|2844/7270|2612/5655|871/1884||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.2471C>T|p.Pro824Leu|2752/7115|2471/5451|824/1816||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2612C>T|p.Pro871Leu|2844/7207|2612/5592|871/1863||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T||||||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1825C>T||||||,A|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2748C>T||||||;COSMIC_ID=COSM3755564;TISSUE=prostate;TUMOR=carcinoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.33539;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 chr17 43093454 . C T 425.77 PASS GENE=BRCA1;AC=2;AF=1;AN=2;DP=11;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=31.78;SOR=1.27;ANN=T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2077G>A|p.Asp693Asn|2309/7270|2077/5655|693/1884||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.1936G>A|p.Asp646Asn|2217/7115|1936/5451|646/1816||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2077G>A|p.Asp693Asn|2309/7207|2077/5592|693/1863||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1290G>A||||||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1290G>A||||||,T|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2213G>A||||||;COSMIC_ID=COSM4989394;TISSUE=soft_tissue;TUMOR=rhabdomyosarcoma_--_embryonal;FATHMM=NEUTRAL;SOMATIC=Reported_in_another_cancer_sample_as_somatic;CHASM_PVALUE=0.0014;CHASM_FDR=0.05;VEST_PVALUE=0.51068;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,11:11:33:454,33,0 chr19 39177761 . G C 1134.77 PASS GENE=PAK4;AC=1;AF=0.5;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=10.71;ReadPosRankSum=1.397;SOR=0.654;ANN=C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014831.2|Coding|10/11|c.1572G>C|p.Met524Ile|2033/3064|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014832.1|Coding|8/9|c.1572G>C|p.Met524Ile|1734/2765|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014834.2|Coding|7/8|c.1113G>C|p.Met371Ile|1275/2306|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014835.1|Coding|8/9|c.1113G>C|p.Met371Ile|1348/2379|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_005884.3|Coding|9/10|c.1572G>C|p.Met524Ile|1807/2838|1572/1776|524/591||;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.01093;VEST_FDR=0.15 GT:AD:DP:GQ:PL 0/1:58,48:106:99:1163,0,1435 chr19 47271515 . T C 336.77 PASS GENE=CCDC9;AC=2;AF=1;AN=2;DP=12;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=28.06;SOR=2.67;ANN=C|missense_variant|MODERATE|CCDC9|CCDC9|transcript|NM_015603.2|Coding|12/12|c.1433T>C|p.Leu478Pro|1640/2078|1433/1596|478/531||;COSMIC_ID=COSM3721172;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.093;CHASM_FDR=0.15;VEST_PVALUE=0.97622;VEST_FDR=1 GT:AD:DP:GQ:PL 1/1:0,12:12:36:365,36,0 chr20 46687147 . C T 423.77 PASS GENE=TP53RK;AC=1;AF=0.5;AN=2;BaseQRankSum=-0.26;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=16.3;ReadPosRankSum=1.395;SOR=1.179;ANN=T|missense_variant|MODERATE|TP53RK|TP53RK|transcript|NM_033550.3|Coding|2/2|c.368G>A|p.Arg123Gln|591/3373|368/762|123/253||;COSMIC_ID=COSM3758608;TISSUE=pancreas;TUMOR=carcinoma_--_ductal_carcinoma;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0834;CHASM_FDR=0.15;VEST_PVALUE=0.88584;VEST_FDR=1 GT:AD:DP:GQ:PL 0/1:8,18:26:99:452,0,165