##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20161214
##fileUTCtime=2016-12-14T00:32:59
##source="tvc 5.0-13 (e975447) - Torrent Variant Caller"
##parametersName="Panel-optimized - Cancer Hotspot Panel v2 [Somatic - High stringency]"
##parametersDetails="custom_external_file, TS version: 5.0"
##basecallerVersion="5.0-13/e975447"
##tmapVersion="5.0.13 (e975447) (201510291545)"
##reference=/results/referenceLibrary/tmap-f3/hg19/hg19.fasta
##phasing=none
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=HS,Number=0,Type=Flag,Description="Indicate it is at a hot spot">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations">
##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##INFO=<ID=SAF,Number=A,Type=Integer,Description="Alternate allele observations on the forward strand">
##INFO=<ID=SAR,Number=A,Type=Integer,Description="Alternate allele observations on the reverse strand">
##INFO=<ID=FDP,Number=1,Type=Integer,Description="Flow Evaluator read depth at the locus">
##INFO=<ID=FRO,Number=1,Type=Integer,Description="Flow Evaluator Reference allele observations">
##INFO=<ID=FAO,Number=A,Type=Integer,Description="Flow Evaluator Alternate allele observations">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency based on Flow Evaluator observation counts">
##INFO=<ID=QD,Number=1,Type=Float,Description="QualityByDepth as 4*QUAL/FDP (analogous to GATK)">
##INFO=<ID=FSRF,Number=1,Type=Integer,Description="Flow Evaluator Reference observations on the forward strand">
##INFO=<ID=FSRR,Number=1,Type=Integer,Description="Flow Evaluator Reference observations on the reverse strand">
##INFO=<ID=FSAF,Number=A,Type=Integer,Description="Flow Evaluator Alternate allele observations on the forward strand">
##INFO=<ID=FSAR,Number=A,Type=Integer,Description="Flow Evaluator Alternate allele observations on the reverse strand">
##INFO=<ID=FXX,Number=1,Type=Float,Description="Flow Evaluator failed read ratio">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=HRUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
##INFO=<ID=FR,Number=.,Type=String,Description="Reason why the variant was filtered.">
##INFO=<ID=RBI,Number=A,Type=Float,Description="Distance of bias parameters from zero.">
##INFO=<ID=FWDB,Number=A,Type=Float,Description="Forward strand bias in prediction.">
##INFO=<ID=REVB,Number=A,Type=Float,Description="Reverse strand bias in prediction.">
##INFO=<ID=REFB,Number=A,Type=Float,Description="Reference Hypothesis bias in prediction.">
##INFO=<ID=VARB,Number=A,Type=Float,Description="Variant Hypothesis bias in prediction.">
##INFO=<ID=SSSB,Number=A,Type=Float,Description="Strand-specific strand bias for allele.">
##INFO=<ID=SSEN,Number=A,Type=Float,Description="Strand-specific-error prediction on negative strand.">
##INFO=<ID=SSEP,Number=A,Type=Float,Description="Strand-specific-error prediction on positive strand.">
##INFO=<ID=STB,Number=A,Type=Float,Description="Strand bias in variant relative to reference.">
##INFO=<ID=STBP,Number=A,Type=Float,Description="Pval of Strand bias in variant relative to reference.">
##INFO=<ID=PB,Number=A,Type=Float,Description="Bias of relative variant position in reference reads versus variant reads. Equals Mann-Whitney U rho statistic P(Y>X)+0.5P(Y=X)">
##INFO=<ID=PBP,Number=A,Type=Float,Description="Pval of relative variant position in reference reads versus variant reads.  Related to GATK ReadPosRankSumTest">
##INFO=<ID=MLLD,Number=A,Type=Float,Description="Mean log-likelihood delta per read.">
##FILTER=<ID=NOCALL,Description="Generic filter. Filtering details stored in FR info tag.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##FORMAT=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##FORMAT=<ID=SAF,Number=A,Type=Integer,Description="Alternate allele observations on the forward strand">
##FORMAT=<ID=SAR,Number=A,Type=Integer,Description="Alternate allele observations on the reverse strand">
##FORMAT=<ID=FDP,Number=1,Type=Integer,Description="Flow Evaluator Read Depth">
##FORMAT=<ID=FRO,Number=1,Type=Integer,Description="Flow Evaluator Reference allele observation count">
##FORMAT=<ID=FAO,Number=A,Type=Integer,Description="Flow Evaluator Alternate allele observation count">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele frequency based on Flow Evaluator observation counts">
##FORMAT=<ID=FSRF,Number=1,Type=Integer,Description="Flow Evaluator reference observations on the forward strand">
##FORMAT=<ID=FSRR,Number=1,Type=Integer,Description="Flow Evaluator reference observations on the reverse strand">
##FORMAT=<ID=FSAF,Number=A,Type=Integer,Description="Flow Evaluator Alternate allele observations on the forward strand">
##FORMAT=<ID=FSAR,Number=A,Type=Integer,Description="Flow Evaluator Alternate allele observations on the reverse strand">
##INFO=<ID=OID,Number=.,Type=String,Description="List of original Hotspot IDs">
##INFO=<ID=OPOS,Number=.,Type=Integer,Description="List of original allele positions">
##INFO=<ID=OREF,Number=.,Type=String,Description="List of original reference bases">
##INFO=<ID=OALT,Number=.,Type=String,Description="List of original variant bases">
##INFO=<ID=OMAPALT,Number=.,Type=String,Description="Maps OID,OPOS,OREF,OALT entries to specific ALT alleles">
##deamination_metric=0.0709972
##bcftools_normVersion=1.3+htslib-1.3
##bcftools_normCommand=norm -m-any -f /home/hugpat/tools/ucsc.hg19.fasta -o /data/DMGL/SPC/OncoBench/analysis_302/TSVC_variants_IonXpress_013.vcf.tmp -O v /data/DMGL/SPC/OncoBench/analysis_302/TSVC_variants_IonXpress_013.vcf.gz
##bcftools_normCommand=norm -m-any -f /home/hugpat/tools/ucsc.hg19.fasta -o /data/DMGL/SPC/OncoBench/analysis_302/TSVC_variants_IonXpress_013.vcf.tmp2 -O v /data/DMGL/SPC/OncoBench/analysis_302/TSVC_variants_IonXpress_013.vcf.tmp
##bcftools_filterVersion=1.3+htslib-1.3
##bcftools_filterCommand=filter -i 'AF>=0.01 & FILTER=='PASS'' -o /data/DMGL/SPC/OncoBench/analysis_302/TSVC_variants_IonXpress_013.vcf.tmp3 -O v /data/DMGL/SPC/OncoBench/analysis_302/TSVC_variants_IonXpress_013.vcf.tmp2
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HUG16-1
chr4	1807894	.	G	A	31740.1	PASS	AF=1;AO=121914;DP=122611;FAO=1986;FDP=1986;FR=.,REALIGNEDx0.9915;FRO=0;FSAF=987;FSAR=999;FSRF=0;FSRR=0;FWDB=0.0820799;FXX=0.00699996;HRUN=1;LEN=1;MLLD=64.1515;OALT=A;OID=.;OMAPALT=A;OPOS=1807894;OREF=G;PB=0.5;PBP=1;QD=63.9277;RBI=0.0835361;REFB=0;REVB=-0.0155295;RO=294;SAF=58896;SAR=63018;SRF=169;SRR=125;SSEN=0;SSEP=0;SSSB=-0.000422629;STB=0.5;STBP=1;TYPE=snp;VARB=-4.81751e-05	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:142:122611:1986:294:0:121914:1986:1:63018:58896:169:125:999:987:0:0
chr4	55141055	COSM12417	A	G	28284.6	PASS	AF=1;AO=139036;DP=155111;FAO=1954;FDP=1954;FR=.;FRO=0;FSAF=1065;FSAR=889;FSRF=0;FSRR=0;FWDB=-0.00658924;FXX=0.0229999;HRUN=1;LEN=1;MLLD=112.277;OALT=-,G;OID=COSM12417,.;OMAPALT=A,AGCCCGGATGGACATG;OPOS=55141051,55141055;OREF=GCCCAGATGGACATG,A;PB=0.5;PBP=1;QD=57.9009;RBI=0.0561734;REFB=0;REVB=0.0557856;RO=77;SAF=82757;SAR=56279;SRF=50;SRR=27;SSEN=0;SSEP=0;SSSB=-5.95334e-05;STB=0.5;STBP=1;TYPE=snp;VARB=1.9211e-05;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:256:155111:1954:77:0:139036:1954:1:56279:82757:50:27:889:1065:0:0
chr5	149433596	.	TG	GA	29472.9	PASS	AF=0.969497;AO=49301;DP=51383;FAO=1907;FDP=1967;FR=.;FRO=60;FSAF=1713;FSAR=194;FSRF=60;FSRR=0;FWDB=0.00206625;FXX=0.0164999;HRUN=1;LEN=2;MLLD=146.082;OALT=GA;OID=.;OMAPALT=GA;OPOS=149433596;OREF=TG;PB=0.5;PBP=1;QD=59.9348;RBI=0.0102449;REFB=0.0285051;REVB=0.0100344;RO=1363;SAF=44416;SAR=4885;SRF=1345;SRR=18;SSEN=0;SSEP=0;SSSB=-0.0124986;STB=0.508606;STBP=0.011;TYPE=mnp;VARB=-0.00107239	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:13:51383:1967:1363:60:49301:1907:0.969497:4885:44416:1345:18:194:1713:60:0
chr7	55242466	COSM26038	GAATTAAGAGA	G	14651.6	PASS	AF=0.691289;AO=165236;DP=250800;FAO=1357;FDP=1963;FR=.;FRO=606;FSAF=814;FSAR=543;FSRF=380;FSRR=226;FWDB=0.00235199;FXX=0.0184999;HRUN=2;LEN=10;MLLD=469.986;OALT=-,-;OID=COSM26038,.;OMAPALT=C,CAAGGA;OPOS=55242463,55242467;OREF=AAGGAATTAAGAGAA,AATTAAGAGA;PB=0.5;PBP=1;QD=29.8555;RBI=0.00913022;REFB=0.00619844;REVB=0.00882207;RO=78469;SAF=97904;SAR=67332;SRF=46527;SRR=31942;SSEN=0;SSEP=0;SSSB=-0.000265433;STB=0.50878;STBP=0.25;TYPE=del;VARB=-0.0028501;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:3785:250800:1963:78469:606:165236:1357:0.691289:67332:97904:46527:31942:543:814:380:226
chr7	55242481	COSM133207	ACATCT	A	13707.6	PASS	AF=0.672191;AO=160214;DP=249402;FAO=1298;FDP=1931;FR=.;FRO=633;FSAF=782;FSAR=516;FSRF=385;FSRR=248;FWDB=-0.00469133;FXX=0.0344998;HRUN=1;LEN=5;MLLD=639.004;OALT=-,-;OID=COSM133207,.;OMAPALT=C,CAACCGAAAGCCAACAAGGA;OPOS=55242482,55242482;OREF=CATCTCCGAAAGCCAACAAGGAAA,CATCT;PB=0.5;PBP=1;QD=28.3947;RBI=0.00654034;REFB=-0.00571341;REVB=-0.00455714;RO=75525;SAF=94443;SAR=65771;SRF=44509;SRR=31016;SSEN=0;SSEP=0;SSSB=9.44794e-05;STB=0.501969;STBP=0.814;TYPE=del;VARB=0.0028714;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:4141:249402:1931:75525:633:160214:1298:0.672191:65771:94443:44509:31016:516:782:385:248
chr7	55249063	.	G	A	31995.8	PASS	AF=1;AO=24508;DP=24564;FAO=1997;FDP=1997;FR=.,REALIGNEDx0.9965;FRO=0;FSAF=807;FSAR=1190;FSRF=0;FSRR=0;FWDB=-0.0175775;FXX=0.00149999;HRUN=1;LEN=1;MLLD=82.9859;OALT=A;OID=.;OMAPALT=A;OPOS=55249063;OREF=G;PB=0.5;PBP=1;QD=64.0877;RBI=0.0194966;REFB=0;REVB=0.00843486;RO=32;SAF=9872;SAR=14636;SRF=12;SRR=20;SSEN=0;SSEP=0;SSSB=7.20381e-05;STB=0.5;STBP=1;TYPE=snp;VARB=1.24056e-06	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:167:24564:1997:32:0:24508:1997:1:14636:9872:12:20:1190:807:0:0
chr7	55249071	COSM6240	C	T	236.275	PASS	AF=0.0830415;AO=2032;DP=24599;FAO=166;FDP=1999;FR=.;FRO=1833;FSAF=68;FSAR=98;FSRF=718;FSRR=1115;FWDB=0.0559036;FXX=0.000499998;HRUN=1;LEN=1;MLLD=266.843;OALT=T;OID=COSM6240;OMAPALT=T;OPOS=55249071;OREF=C;PB=0.5;PBP=1;QD=0.472786;RBI=0.0560458;REFB=0.000563192;REVB=-0.00398909;RO=22496;SAF=783;SAR=1249;SRF=8940;SRR=13556;SSEN=0;SSEP=0;SSSB=-0.014979;STB=0.5171;STBP=0.661;TYPE=snp;VARB=-0.00673451;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:236:24599:1999:22496:1833:2032:166:0.0830415:1249:783:8940:13556:98:68:718:1115
chr10	43613843	.	G	T	31918	PASS	AF=1;AO=163766;DP=164324;FAO=1993;FDP=1993;FR=.,REALIGNEDx0.9625;FRO=0;FSAF=1045;FSAR=948;FSRF=0;FSRR=0;FWDB=0.157587;FXX=0.00349998;HRUN=1;LEN=1;MLLD=273.842;OALT=T;OID=.;OMAPALT=T;OPOS=43613843;OREF=G;PB=0.5;PBP=1;QD=64.0601;RBI=0.15801;REFB=0;REVB=0.0115538;RO=150;SAF=83478;SAR=80288;SRF=141;SRR=9;SSEN=0;SSEP=0;SSSB=-0.000753524;STB=0.5;STBP=1;TYPE=snp;VARB=1.037e-05	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:169:164324:1993:150:0:163766:1993:1:80288:83478:141:9:948:1045:0:0
chr11	534242	COSM249860	A	G	8155.89	PASS	AF=0.479479;AO=39771;DP=76903;FAO=958;FDP=1998;FR=.;FRO=1040;FSAF=525;FSAR=433;FSRF=516;FSRR=524;FWDB=-0.0158133;FXX=0.000999995;HRUN=4;LEN=1;MLLD=217.83;OALT=G;OID=COSM249860;OMAPALT=G;OPOS=534242;OREF=A;PB=0.5;PBP=1;QD=16.3281;RBI=0.0158141;REFB=0.0105034;REVB=0.000153654;RO=36645;SAF=20361;SAR=19410;SRF=18187;SRR=18458;SSEN=0;SSEP=0;SSSB=0.0138099;STB=0.527105;STBP=0.028;TYPE=snp;VARB=-0.0119215;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:8155:76903:1998:36645:1040:39771:958:0.479479:19410:20361:18187:18458:433:525:516:524
chr17	7579472	COSM45985	G	C	8690.46	PASS	AF=0.899329;AO=658;DP=742;FAO=670;FDP=745;FR=.;FRO=75;FSAF=251;FSAR=419;FSRF=20;FSRR=55;FWDB=0.00471464;FXX=0.00134046;HRUN=6;LEN=1;MLLD=231.736;OALT=C,T;OID=.,COSM45985;OMAPALT=C,T;OPOS=7579472,7579472;OREF=G,G;PB=0.5;PBP=1;QD=46.6602;RBI=0.0141981;REFB=-0.00647363;REVB=-0.0133925;RO=75;SAF=250;SAR=408;SRF=20;SRR=55;SSEN=0;SSEP=0;SSSB=0.0235313;STB=0.511665;STBP=0.062;TYPE=snp;VARB=0.000464411;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:155:742:745:75:75:658:670:0.899329:408:250:20:55:419:251:20:55
chr17	7579473	COSM44018	G	C	138.364	PASS	AF=0.0955585;AO=66;DP=738;FAO=71;FDP=743;FR=.;FRO=672;FSAF=16;FSAR=55;FSRF=256;FSRR=416;FWDB=-0.0451664;FXX=0.00402139;HRUN=6;LEN=1;MLLD=64.844;OALT=A,C;OID=COSM44018,.;OMAPALT=A,C;OPOS=7579473,7579473;OREF=G,G;PB=0.5;PBP=1;QD=0.744891;RBI=0.0451941;REFB=-0.0357252;REVB=0.00158294;RO=672;SAF=15;SAR=51;SRF=256;SRR=416;SSEN=0;SSEP=0;SSSB=-0.208991;STB=0.664957;STBP=0.001;TYPE=snp;VARB=0.0615014;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:135:738:743:672:672:66:71:0.0955585:51:15:256:416:55:16:256:416
chr19	1220321	.	T	C	30970.8	PASS	AF=0.984304;AO=59651;DP=69446;FAO=1944;FDP=1975;FR=.,HEALED;FRO=0;FSAF=1103;FSAR=841;FSRF=0;FSRR=0;FWDB=0.034408;FXX=0.0124999;HRUN=1;LEN=1;MLLD=232.153;OALT=C;OID=.;OMAPALT=C;OPOS=1220321;OREF=T;PB=0.5;PBP=1;QD=62.7257;RBI=0.0414961;REFB=0;REVB=0.0231952;RO=151;SAF=31700;SAR=27951;SRF=139;SRR=12;SSEN=0;SSEP=0;SSSB=-0.00188704;STB=0.5;STBP=1;TYPE=snp;VARB=0.000544465	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:3:69446:1975:151:0:59651:1944:0.984304:27951:31700:139:12:841:1103:0:0