##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20161213
##fileUTCtime=2016-12-13T21:09:50
##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=0.831509
##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_297/TSVC_variants_IonXpress_009.vcf.tmp -O v /data/DMGL/SPC/OncoBench/analysis_297/TSVC_variants_IonXpress_009.vcf.gz
##bcftools_normCommand=norm -m-any -f /home/hugpat/tools/ucsc.hg19.fasta -o /data/DMGL/SPC/OncoBench/analysis_297/TSVC_variants_IonXpress_009.vcf.tmp2 -O v /data/DMGL/SPC/OncoBench/analysis_297/TSVC_variants_IonXpress_009.vcf.tmp
##bcftools_filterVersion=1.3+htslib-1.3
##bcftools_filterCommand=filter -i 'AF>=0.01 & FILTER=='PASS'' -o /data/DMGL/SPC/OncoBench/analysis_297/TSVC_variants_IonXpress_009.vcf.tmp3 -O v /data/DMGL/SPC/OncoBench/analysis_297/TSVC_variants_IonXpress_009.vcf.tmp2
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HUG16-2
chr3	41266097	COSM5672;COSM5668;COSM5661	G	A	103.51	PASS	AF=0.010846;AO=20;DP=1844;FAO=20;FDP=1844;FR=.,REALIGNEDx0.01627;FRO=1824;FSAF=5;FSAR=15;FSRF=754;FSRR=1070;FWDB=0.0169687;FXX=0;HRUN=2;LEN=1;MLLD=80.7201;OALT=A,C,T;OID=COSM5672,COSM5668,COSM5661;OMAPALT=A,C,T;OPOS=41266097,41266097,41266097;OREF=G,G,G;PB=0.5;PBP=1;QD=0.224533;RBI=0.0480671;REFB=0.000341971;REVB=0.0449724;RO=1822;SAF=5;SAR=15;SRF=752;SRR=1070;SSEN=0;SSEP=0;SSSB=-0.0643279;STB=0.677087;STBP=0.135;TYPE=snp;VARB=-0.0499108;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/0:101:1844:1844:1822:1824:20:20:0.010846:15:5:752:1070:15:5:754:1070
chr3	178952085	COSM775;COSM94986;COSM776;COSM94987	A	G	921.646	PASS	AF=0.145218;AO=2187;DP=14485;FAO=290;FDP=1997;FR=.,REALIGNEDx0.157;FRO=1707;FSAF=131;FSAR=159;FSRF=573;FSRR=1134;FWDB=0.0840836;FXX=0.00149999;HRUN=1;LEN=1;MLLD=97.5902;OALT=G,T,G,T;OID=COSM775,COSM776,COSM94986,COSM94987;OMAPALT=G,T,G,T;OPOS=178952085,178952085,178952085,178952085;OREF=A,A,A,A;PB=0.5;PBP=1;QD=1.84606;RBI=0.0843216;REFB=0.00126375;REVB=0.00633129;RO=12260;SAF=1004;SAR=1183;SRF=4149;SRR=8111;SSEN=0;SSEP=0;SSSB=0.163504;STB=0.602096;STBP=0.001;TYPE=snp;VARB=-0.00765412;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:921:14485:1997:12260:1707:2187:290:0.145218:1183:1004:4149:8111:159:131:573:1134
chr4	1807894	.	G	A	31698.2	PASS	AF=1;AO=45088;DP=45235;FAO=1984;FDP=1984;FR=.,REALIGNEDx0.994;FRO=0;FSAF=989;FSAR=995;FSRF=0;FSRR=0;FWDB=0.0733878;FXX=0.00799996;HRUN=1;LEN=1;MLLD=66.28;OALT=A;OID=.;OMAPALT=A;OPOS=1807894;OREF=G;PB=0.5;PBP=1;QD=63.9077;RBI=0.0771734;REFB=0;REVB=-0.0238739;RO=38;SAF=21651;SAR=23437;SRF=24;SRR=14;SSEN=0;SSEP=0;SSSB=-0.000244224;STB=0.5;STBP=1;TYPE=snp;VARB=-6.38659e-05	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:150:45235:1984:38:0:45088:1984:1:23437:21651:24:14:995:989:0:0
chr4	55141055	COSM12417	A	G	27930.8	PASS	AF=1;AO=4134;DP=4724;FAO=1929;FDP=1929;FR=.;FRO=0;FSAF=1074;FSAR=855;FSRF=0;FSRR=0;FWDB=0.00426521;FXX=0.0354998;HRUN=1;LEN=1;MLLD=112.239;OALT=-,G;OID=COSM12417,.;OMAPALT=A,AGCCCGGATGGACATG;OPOS=55141051,55141055;OREF=GCCCAGATGGACATG,A;PB=0.5;PBP=1;QD=57.9177;RBI=0.0566884;REFB=0;REVB=0.0565277;RO=3;SAF=2471;SAR=1663;SRF=1;SRR=2;SSEN=0;SSEP=0;SSSB=0.000381247;STB=0.5;STBP=1;TYPE=snp;VARB=2.45027e-05;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	1/1:229:4724:1929:3:0:4134:1929:1:1663:2471:1:2:855:1074:0:0
chr4	55152040	COSM22413	C	T	19.7468	PASS	AF=0.0255;AO=498;DP=19089;FAO=51;FDP=2000;FR=.,REALIGNEDx0.034;FRO=1949;FSAF=24;FSAR=27;FSRF=1035;FSRR=914;FWDB=0.0535141;FXX=0;HRUN=2;LEN=1;MLLD=60.3665;OALT=T;OID=COSM22413;OMAPALT=T;OPOS=55152040;OREF=C;PB=0.5;PBP=1;QD=0.0394937;RBI=0.0565613;REFB=0.00138967;REVB=0.0183145;RO=18587;SAF=285;SAR=213;SRF=10220;SRR=8367;SSEN=0;SSEP=0;SSSB=0.0161227;STB=0.558685;STBP=0.41;TYPE=snp;VARB=-0.0654898;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/0:19:19089:2000:18587:1949:498:51:0.0255:213:285:10220:8367:27:24:1035:914
chr4	55980239	.	C	T	22199	PASS	AF=0.936182;AO=1416;DP=1532;FAO=1643;FDP=1755;FR=.,REALIGNEDx0.9539;FRO=112;FSAF=1607;FSAR=36;FSRF=86;FSRR=26;FWDB=0.117594;FXX=0.0011383;HRUN=1;LEN=1;MLLD=54.4696;OALT=T;OID=.;OMAPALT=T;OPOS=55980239;OREF=C;PB=0.5;PBP=1;QD=50.5961;RBI=0.122103;REFB=-0.142998;REVB=-0.032877;RO=112;SAF=1380;SAR=36;SRF=86;SRR=26;SSEN=0;SSEP=0;SSSB=0.223481;STB=0.620454;STBP=0;TYPE=snp;VARB=0.0203994	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:195:1532:1755:112:112:1416:1643:0.936182:36:1380:86:26:36:1607:86:26
chr5	112175770	COSM19714;COSM19626;COSM19349	G	A	9567.04	PASS	AF=0.52953;AO=4210;DP=8179;FAO=1058;FDP=1998;FR=.,REALIGNEDx0.5335;FRO=940;FSAF=580;FSAR=478;FSRF=533;FSRR=407;FWDB=-0.010469;FXX=0.000999995;HRUN=2;LEN=1;MLLD=224.686;OALT=-,A,-,-;OID=COSM19349,.,COSM19714,COSM19626;OMAPALT=C,CAG,CG,CG;OPOS=112175770,112175770,112175770,112175771;OREF=GG,G,G,G;PB=0.5;PBP=1;QD=19.1532;RBI=0.032766;REFB=0.00978166;REVB=-0.0310485;RO=3845;SAF=2341;SAR=1869;SRF=2242;SRR=1603;SSEN=0;SSEP=0;SSSB=-0.0241231;STB=0.508951;STBP=0.416;TYPE=snp;VARB=-0.00897714;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:7884:8179:1998:3845:940:4210:1058:0.52953:1869:2341:2242:1603:478:580:533:407
chr5	149433596	.	TG	GA	29824.2	PASS	AF=0.973165;AO=3534;DP=3688;FAO=1922;FDP=1975;FR=.;FRO=53;FSAF=1711;FSAR=211;FSRF=28;FSRR=25;FWDB=-0.00139773;FXX=0.0124999;HRUN=1;LEN=2;MLLD=165.123;OALT=GA;OID=.;OMAPALT=GA;OPOS=149433596;OREF=TG;PB=0.5;PBP=1;QD=60.4034;RBI=0.00692816;REFB=-0.0145783;REVB=0.00678571;RO=107;SAF=3137;SAR=397;SRF=59;SRR=48;SSEN=0;SSEP=0;SSSB=0.0454977;STB=0.523917;STBP=0;TYPE=mnp;VARB=0.000417389	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:5:3688:1975:107:53:3534:1922:0.973165:397:3137:59:48:211:1711:28:25
chr7	55242457	COSM26509	G	A	107.471	PASS	AF=0.011;AO=24;DP=2196;FAO=22;FDP=2000;FR=.;FRO=1978;FSAF=14;FSAR=8;FSRF=1250;FSRR=728;FWDB=0.02218;FXX=0;HRUN=1;LEN=1;MLLD=84.0962;OALT=A;OID=COSM26509;OMAPALT=A;OPOS=55242457;OREF=G;PB=0.5;PBP=1;QD=0.214942;RBI=0.0231144;REFB=0.000349794;REVB=0.00650544;RO=2168;SAF=16;SAR=8;SRF=1362;SRR=806;SSEN=0;SSEP=0;SSSB=0.0157648;STB=0.504698;STBP=0.974;TYPE=snp;VARB=-0.0377651;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/0:107:2196:2000:2168:1978:24:22:0.011:8:16:1362:806:8:14:1250:728
chr7	55248995	COSM28603	G	A	48.5188	PASS	AF=0.0119435;AO=11;DP=920;FAO=11;FDP=921;FR=.;FRO=910;FSAF=3;FSAR=8;FSRF=315;FSRR=595;FWDB=-0.00383735;FXX=0;HRUN=1;LEN=1;MLLD=138.772;OALT=A;OID=COSM28603;OMAPALT=A;OPOS=55248995;OREF=G;PB=0.5;PBP=1;QD=0.210722;RBI=0.0135507;REFB=0.00019834;REVB=-0.0129961;RO=909;SAF=3;SAR=8;SRF=315;SRR=594;SSEN=0;SSEP=0;SSSB=-0.0333989;STB=0.584263;STBP=0.633;TYPE=snp;VARB=-0.0334948;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/0:48:920:921:909:910:11:11:0.0119435:8:3:315:594:8:3:315:595
chr7	55249063	.	G	A	4412.97	PASS	AF=0.478587;AO=443;DP=933;FAO=447;FDP=934;FR=.,REALIGNEDx0.4807;FRO=487;FSAF=148;FSAR=299;FSRF=160;FSRR=327;FWDB=0.0010964;FXX=0;HRUN=1;LEN=1;MLLD=73.3379;OALT=A;OID=.;OMAPALT=A;OPOS=55249063;OREF=G;PB=0.5;PBP=1;QD=18.8992;RBI=0.00611993;REFB=-0.00342494;REVB=-0.00602091;RO=487;SAF=147;SAR=296;SRF=160;SRR=327;SSEN=0;SSEP=0;SSSB=0.00354181;STB=0.501505;STBP=0.925;TYPE=snp;VARB=0.00361066	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:4412:933:934:487:487:443:447:0.478587:296:147:160:327:299:148:160:327
chr10	43613843	.	G	T	9858.17	PASS	AF=0.490245;AO=17947;DP=36051;FAO=980;FDP=1999;FR=.,REALIGNEDx0.491;FRO=1019;FSAF=492;FSAR=488;FSRF=511;FSRR=508;FWDB=0.0811163;FXX=0.000499998;HRUN=1;LEN=1;MLLD=276.696;OALT=T;OID=.;OMAPALT=T;OPOS=43613843;OREF=G;PB=0.5;PBP=1;QD=19.7262;RBI=0.0811756;REFB=-0.0238301;REVB=0.00310172;RO=17995;SAF=8896;SAR=9051;SRF=8617;SRR=9378;SSEN=0;SSEP=0;SSSB=0.0154465;STB=0.50029;STBP=0.981;TYPE=snp;VARB=0.0248758	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:9858:36051:1999:17995:1019:17947:980:0.490245:9051:8896:8617:9378:488:492:511:508
chr11	108172402	.	C	T	58.8482	PASS	AF=0.0425;AO=809;DP=17998;FAO=85;FDP=2000;FR=.,REALIGNEDx0.0615;FRO=1915;FSAF=35;FSAR=50;FSRF=938;FSRR=977;FWDB=0.049051;FXX=0;HRUN=2;LEN=1;MLLD=71.8457;OALT=T;OID=.;OMAPALT=T;OPOS=108172402;OREF=C;PB=0.5;PBP=1;QD=0.117696;RBI=0.0490735;REFB=0.000742826;REVB=0.00148646;RO=17117;SAF=357;SAR=452;SRF=8298;SRR=8819;SSEN=0;SSEP=0;SSSB=-0.0414708;STB=0.575075;STBP=0.136;TYPE=snp;VARB=-0.0197274	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:58:17998:2000:17117:1915:809:85:0.0425:452:357:8298:8819:50:35:938:977
chr12	25398284	COSM520;COSM522;COSM521;COSM512;COSM514;COSM34144;COSM25081	C	T	48.4849	PASS	AF=0.053;AO=785;DP=14955;FAO=106;FDP=2000;FR=.,REALIGNEDx0.061;FRO=1894;FSAF=53;FSAR=53;FSRF=999;FSRR=895;FWDB=0.00237646;FXX=0;HRUN=2;LEN=2;MLLD=260.159;OALT=AA,A,AG,AT,G,TA,T;OID=COSM512,COSM520,COSM514,COSM34144,COSM522,COSM25081,COSM521;OMAPALT=AA,AC,AG,AT,GC,TA,TC;OPOS=25398284,25398284,25398284,25398284,25398284,25398284,25398284;OREF=CC,C,CC,CC,C,CC,C;PB=0.5;PBP=1;QD=0.0969698;RBI=0.0229239;REFB=-0.00112563;REVB=-0.0228004;RO=14123;SAF=378;SAR=407;SRF=7515;SRR=6608;SSEN=0;SSEP=0;SSSB=-0.0514296;STB=0.525995;STBP=0.556;TYPE=snp;VARB=0.0222011;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:49:14955:2000:14123:1894:785:106:0.053:407:378:7515:6608:53:53:999:895
chr13	28610183	.	A	G	11238.9	PASS	AF=0.534;AO=27396;DP=49600;FAO=1068;FDP=2000;FR=.;FRO=932;FSAF=402;FSAR=666;FSRF=413;FSRR=519;FWDB=0.0174088;FXX=0;HRUN=1;LEN=1;MLLD=89.9759;OALT=G;OID=.;OMAPALT=G;OPOS=28610183;OREF=A;PB=0.5;PBP=1;QD=22.4778;RBI=0.0179212;REFB=-0.018022;REVB=-0.00425505;RO=22154;SAF=11000;SAR=16396;SRF=9648;SRR=12506;SSEN=0;SSEP=0;SSSB=-0.0290158;STB=0.532585;STBP=0.002;TYPE=snp;VARB=0.0166052	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/1:9108:49600:2000:22154:932:27396:1068:0.534:16396:11000:9648:12506:666:402:413:519
chr17	7577027	COSM45128;COSM44417	G	A	55.0629	PASS	AF=0.0117532;AO=12;DP=1022;FAO=12;FDP=1021;FR=.;FRO=1009;FSAF=4;FSAR=8;FSRF=546;FSRR=463;FWDB=-0.0151636;FXX=0.000978464;HRUN=1;LEN=1;MLLD=189.785;OALT=A,-;OID=COSM45128,COSM44417;OMAPALT=AT,G;OPOS=7577027,7577028;OREF=G,T;PB=0.5;PBP=1;QD=0.215722;RBI=0.0166006;REFB=1.405e-05;REVB=0.00675624;RO=1009;SAF=4;SAR=8;SRF=546;SRR=463;SSEN=0;SSEP=0;SSSB=-0.0831664;STB=0.699869;STBP=0.182;TYPE=snp;VARB=-0.001317;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/0:54:1022:1021:1009:1009:12:12:0.0117532:8:4:546:463:8:4:546:463
chr22	24176287	COSM1090	G	A	81.1588	PASS	AF=0.0126147;AO=22;DP=1745;FAO=22;FDP=1744;FR=.,REALIGNEDx0.02006;FRO=1722;FSAF=14;FSAR=8;FSRF=737;FSRR=985;FWDB=-0.0008926;FXX=0.000573063;HRUN=3;LEN=1;MLLD=67.1788;OALT=A;OID=COSM1090;OMAPALT=A;OPOS=24176287;OREF=G;PB=0.5;PBP=1;QD=0.186144;RBI=0.0454218;REFB=5.42281e-05;REVB=0.045413;RO=1720;SAF=14;SAR=8;SRF=737;SRR=983;SSEN=0;SSEP=0;SSSB=0.0891375;STB=0.698071;STBP=0.064;TYPE=snp;VARB=-0.00492399;HS	GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR	0/0:81:1745:1744:1720:1722:22:22:0.0126147:8:14:737:983:8:14:737:985