##fileformat=VCFv4.2
##fileDate=00000000
##center="NCI Genomic Data Commons (GDC)"
##gdcWorkflow=<ID=somatic_mutation_calling_workflow,Name=mutect2,Description="MuTect2 Somatic Mutation Calling",Version=1.0>
##gdcWorkflow=<ID=somatic_annotation_workflow,Name=mutect2_annotation,Description="VEP Annotation",Version=1.0>
##INDIVIDUAL=<NAME=TCGA-00-0000,ID=00000000-0000-0000-0000-000000000000>
##SAMPLE=<ID=NORMAL,NAME=TCGA-00-0000-000-000-0000-00,ALIQUOT_ID=00000000-0000-0000-0000-000000000000,BAM_ID=00000000-0000-0000-0000-000000000000>
##SAMPLE=<ID=TUMOR,NAME=TCGA-00-0000-000-000-0000-00,ALIQUOT_ID=00000000-0000-0000-0000-000000000000,BAM_ID=00000000-0000-0000-0000-000000000000>
##FILTER=<ID=alt_allele_in_normal,Description="Evidence seen in the normal sample">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=homologous_mapping_event,Description="More than three events were observed in the tumor">
##FILTER=<ID=multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal">
##FILTER=<ID=panel_of_normals,Description="Seen in at least 2 samples in the panel of normals">
##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=t_lod_fstar,Description="Tumor does not meet likelihood threshold">
##FILTER=<ID=triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele fraction of the event in the tumor">
##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the alternate allele">
##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the alternate allele">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description="Fraction of alt reads indicating OxoG error">
##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">
##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=QSS,Number=A,Type=Integer,Description="Sum of base quality scores for each allele">
##FORMAT=<ID=REF_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the reference allele">
##FORMAT=<ID=REF_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the reference allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=ECNT,Number=1,Type=String,Description="Number of events in this haplotype">
##INFO=<ID=HCNT,Number=1,Type=String,Description="Number of haplotypes that support this variant">
##INFO=<ID=MAX_ED,Number=1,Type=Integer,Description="Maximum distance between events in this active region">
##INFO=<ID=MIN_ED,Number=1,Type=Integer,Description="Minimum distance between events in this active region">
##INFO=<ID=NLOD,Number=1,Type=String,Description="Normal LOD score">
##INFO=<ID=PON,Number=1,Type=String,Description="Count from Panel of Normals">
##INFO=<ID=RPA,Number=.,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=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=TLOD,Number=1,Type=String,Description="Tumor LOD score">
##reference=GRCh38.d1.vd1.fa
##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>
##contig=<ID=chr2,length=242193529,assembly=GRCh38.d1.vd1>
##contig=<ID=chr3,length=198295559,assembly=GRCh38.d1.vd1>
##contig=<ID=chr4,length=190214555,assembly=GRCh38.d1.vd1>
##contig=<ID=chr5,length=181538259,assembly=GRCh38.d1.vd1>
##contig=<ID=chr6,length=170805979,assembly=GRCh38.d1.vd1>
##contig=<ID=chr7,length=159345973,assembly=GRCh38.d1.vd1>
##contig=<ID=chr8,length=145138636,assembly=GRCh38.d1.vd1>
##contig=<ID=chr9,length=138394717,assembly=GRCh38.d1.vd1>
##contig=<ID=chr10,length=133797422,assembly=GRCh38.d1.vd1>
##contig=<ID=chr11,length=135086622,assembly=GRCh38.d1.vd1>
##contig=<ID=chr12,length=133275309,assembly=GRCh38.d1.vd1>
##contig=<ID=chr13,length=114364328,assembly=GRCh38.d1.vd1>
##contig=<ID=chr14,length=107043718,assembly=GRCh38.d1.vd1>
##contig=<ID=chr15,length=101991189,assembly=GRCh38.d1.vd1>
##contig=<ID=chr16,length=90338345,assembly=GRCh38.d1.vd1>
##contig=<ID=chr17,length=83257441,assembly=GRCh38.d1.vd1>
##contig=<ID=chr18,length=80373285,assembly=GRCh38.d1.vd1>
##contig=<ID=chr19,length=58617616,assembly=GRCh38.d1.vd1>
##contig=<ID=chr20,length=64444167,assembly=GRCh38.d1.vd1>
##contig=<ID=chr21,length=46709983,assembly=GRCh38.d1.vd1>
##contig=<ID=chr22,length=50818468,assembly=GRCh38.d1.vd1>
##contig=<ID=chrX,length=156040895,assembly=GRCh38.d1.vd1>
##contig=<ID=chrY,length=57227415,assembly=GRCh38.d1.vd1>
##contig=<ID=chrM,length=16569,assembly=GRCh38.d1.vd1>
##VEP=v84 cache=/var/lib/cwl/job508096045_cache/gdc_vep_cache/homo_sapiens/84_GRCh38 db=. regbuild=13.0 sift=sift5.2.2 assembly=GRCh38.p5 gencode=GENCODE 22 genebuild=2014-07 polyphen=2.2.2 ESP=20141103 COSMIC=75 HGMD-PUBLIC=20154 dbSNP=146 ClinVar=201601
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|GMAF|AFR_MAF|AMR_MAF|EAS_MAF|EUR_MAF|SAS_MAF|AA_MAF|EA_MAF|ExAC_MAF|ExAC_Adj_MAF|ExAC_AFR_MAF|ExAC_AMR_MAF|ExAC_EAS_MAF|ExAC_FIN_MAF|ExAC_NFE_MAF|ExAC_OTH_MAF|ExAC_SAS_MAF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|ENTREZ|EVIDENCE">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
chr7	140753336	.	A	T	.	PASS	DB;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=35.51;TLOD=120.26;CSQ=T|missense_variant&NMD_transcript_variant|MODERATE|BRAF|ENSG00000157764|Transcript|ENST00000479537|nonsense_mediated_decay|2/6||ENST00000479537.4:c.83T>A|ENSP00000418033.1:p.Val28Glu|83/743|83/309|28/102|V/E|gTg/gAg|.|1||-1|cds_start_NF|SNV|HGNC|HGNC:1097||5|||ENSP00000418033||H7C4S5|UPI0001B79280|||deleterious(0.01)|possibly_damaging(0.676)|Pfam_domain:PF00069&Pfam_domain:PF07714&PROSITE_profiles:PS50011&Superfamily_domains:SSF56112|||||||||||||||||||pathogenic|1|1|21499247|||||673|,T|missense_variant|MODERATE|BRAF|ENSG00000157764|Transcript|ENST00000288602|protein_coding|15/18||ENST00000288602.9:c.1799T>A|ENSP00000288602.6:p.Val600Glu|1860/2480|1799/2301|600/766|V/E|gTg/gAg|.|1||-1||SNV|HGNC|HGNC:1097|YES|1||CCDS5863.1|ENSP00000288602|P15056||UPI000013DF26|NM_004333.4||deleterious(0)|probably_damaging(0.967)|Pfam_domain:PF07714&Pfam_domain:PF00069&SMART_domains:SM00220&SMART_domains:SM00219&PROSITE_profiles:PS50011&Superfamily_domains:SSF56112|||||||||||||||||||pathogenic|1|1|21499247|||||673|,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|BRAF|ENSG00000157764|Transcript|ENST00000497784|nonsense_mediated_decay|16/19||ENST00000497784.1:c.*1249T>A||1834/2336|-/585|-/194|||.|1||-1|cds_start_NF|SNV|HGNC|HGNC:1097||5|||ENSP00000420119||H7C5K3|UPI0001B79281||||||||||||||||||||||||pathogenic|1|1|21499247|||||673|,T|missense_variant|MODERATE|BRAF|ENSG00000157764|Transcript|ENST00000496384|protein_coding|6/10||ENST00000496384.5:c.622T>A|ENSP00000419060.1:p.Val208Glu|622/8294|623/1128|208/375|V/E|gTg/gAg|.|1||-1|cds_start_NF|SNV|HGNC|HGNC:1097||5|||ENSP00000419060||H7C560|UPI0001B7927F|||deleterious(0)|possibly_damaging(0.792)|Pfam_domain:PF07714&Pfam_domain:PF00069&PROSITE_profiles:PS50011&SMART_domains:SM00220&SMART_domains:SM00219&Superfamily_domains:SSF56112|||||||||||||||||||pathogenic|1|1|21499247|||||673|	GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1	0/0:121,0:0.00:0:0:.:4114,0:54:67	0/1:30,37:0.538:15:22:0.595:1003,1309:14:16
chr7	143935732	.	C	A	.	PASS	ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=53.78;TLOD=245.51;CSQ=A|missense_variant|MODERATE|OR2F2|ENSG00000221910|Transcript|ENST00000408955|protein_coding|1/1||ENST00000408955.2:c.500C>A|ENSP00000386222.2:p.Pro167His|567/1114|500/954|167/317|P/H|cCc/cAc||1||1||SNV|HGNC|HGNC:8247|YES|||CCDS43666.1|ENSP00000386222|O95006||UPI0000041C25|NM_001004685.1||deleterious(0)|possibly_damaging(0.81)|Pfam_domain:PF00001&PROSITE_profiles:PS50262&Superfamily_domains:SSF81321|||||||||||||||||||||||||||135948|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00002090353|promoter_flanking_region|||||||||||1||||SNV|||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1	0/0:179,0:0.00:0:0:.:5596,0:95:84	0/1:77,77:0.503:41:36:0.468:2595,2551:38:39
chr7	149178678	.	T	C	.	PASS	ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=74.85;TLOD=218.89;CSQ=C|missense_variant|MODERATE|ZNF398|ENSG00000197024|Transcript|ENST00000475153|protein_coding|6/6||ENST00000475153.4:c.806T>C|ENSP00000420418.1:p.Leu269Pro|1073/2860|806/1929|269/642|L/P|cTt/cCt||1||1||SNV|HGNC|HGNC:18373|YES|1||CCDS5894.1|ENSP00000420418|Q8TD17|A0A090N7S8|UPI000000DA2F|NM_170686.2||tolerated(0.26)|possibly_damaging(0.779)||||||||||||||||||||||||||||57541|,C|missense_variant|MODERATE|ZNF398|ENSG00000197024|Transcript|ENST00000426851|protein_coding|7/7||ENST00000426851.5:c.293T>C|ENSP00000389972.2:p.Leu98Pro|1144/5268|293/1416|98/471|L/P|cTt/cCt||1||1||SNV|HGNC|HGNC:18373||1||CCDS47739.1|ENSP00000389972|Q8TD17|A0A090N8F2|UPI000002B73E|NM_020781.3||tolerated(0.1)|possibly_damaging(0.779)||||||||||||||||||||||||||||57541|,C|missense_variant|MODERATE|ZNF398|ENSG00000197024|Transcript|ENST00000491174|protein_coding|7/7||ENST00000491174.1:c.293T>C|ENSP00000419391.1:p.Leu98Pro|972/2232|293/1416|98/471|L/P|cTt/cCt||1||1||SNV|HGNC|HGNC:18373||2||CCDS47739.1|ENSP00000419391|Q8TD17|A0A090N8F2|UPI000002B73E|||tolerated(0.1)|possibly_damaging(0.779)||||||||||||||||||||||||||||57541|,C|missense_variant|MODERATE|ZNF398|ENSG00000197024|Transcript|ENST00000483892|protein_coding|6/6||ENST00000483892.4:c.293T>C|ENSP00000418564.1:p.Leu98Pro|916/2121|293/1416|98/471|L/P|cTt/cCt||1||1||SNV|HGNC|HGNC:18373||5||CCDS47739.1|ENSP00000418564|Q8TD17|A0A090N8F2|UPI000002B73E|||tolerated(0.1)|possibly_damaging(0.779)||||||||||||||||||||||||||||57541|	GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1	0/0:254,0:0.00:0:0:.:9317,0:115:139	0/1:82,66:0.455:34:32:0.515:3021,2309:37:45
chr7	152649272	.	T	G	.	PASS	ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=33.86;TLOD=110.91;CSQ=G|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|XRCC2|ENSG00000196584|Transcript|ENST00000495707|processed_transcript|3/3||ENST00000495707.1:n.235A>C||235/4728||||||1||-1||SNV|HGNC|HGNC:12829||1||||||||||||||||||||||||||||||||||||||7516|,G|missense_variant|MODERATE|XRCC2|ENSG00000196584|Transcript|ENST00000359321|protein_coding|3/3||ENST00000359321.1:c.213A>C|ENSP00000352271.1:p.Glu71Asp|299/3067|213/843|71/280|E/D|gaA/gaC||1||-1||SNV|HGNC|HGNC:12829|YES|1||CCDS5933.1|ENSP00000352271|O43543||UPI000000D9C8|NM_005431.1||tolerated(0.59)|benign(0.038)|Pfam_domain:PF08423&PROSITE_profiles:PS50162&Superfamily_domains:SSF52540|||||||||||||||||||||||||||7516|	GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1	0/0:114,0:0.00:0:0:.:3947,0:44:70	0/1:60,40:0.409:19:21:0.475:2024,1282:24:36