UVC results

[kokyriakidis]

Hi!

I have a tumor-only sample and I got the following variants from uvc, all in the same position. UVC cannot detect which of these representations is correct? Moreover, I want to detect indels. Are there any filters, or metrics that I need to watch, to guaranty that these variants are not artifacts?

chr1    2494541 .   A   AG  11.000000   Q20 ANY_VAR;SomaticQ=11;TLODQ=11;NLODQ=119;NLODV=<NONE>;TNBQF=0,-70,0,11;TNCQF=0,0,0,0;tbDP=1812;tDP=1283;tAD=1276,3;t2DP=0;t2AD=0,0;RU=G;RC=6;R3X2=2494535,1,1,2494547,2,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-81:_A_:1283:1276,3:1812:1805,3:0:0,0:_Aa:2312,7,5,7,5,0,59,4,2110,0,0,0:24294,120,337758,12,7,5,700,500:_Ab:28,7,5,5:119719,814,285713,1486:102372,207765,7,5:_Ac:7,6:474,370,564,438:73,98,96,128:38,43,88,93:150,175,369,394:_AQ:136362,300:136962:50798,120:51062:28344,73:28453:_ADPf:770,2:773,0:444,1:445,0:_ADPr:692,1:696,0:368,1:370,0:_ALP:1154,3:1158:1010,3:1014:110978,203:111307:_ARP:1238,4:1246:1162,4:1170:188947,483:190066:_ALB:2009,5:1953,3:1961:443459,829:444794:_ARB:2009,5:1985,5:1995:798967,2025:803779:_ALI:519,1:457,0:457:812,2:815:_ARI:1333,3:1148,1:1153:1462,3:1469:_AX:2274,5:2284:227400,500:228400:2009,5:2019:2274,5:2284:_Ax:227400,500:119238,102:278777,449:2111,5:2236,5:_BDP:939,2:942,0:866,1:870,0:_BT:220737,475:221410:210704,117:211453:5069,46:5138:6490,19:6601:_CDP1:672,2:675,0:604,1:608,0:672,2:675,0:604,1:608,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:34,38:50624,120:28245,73:0,0:0,0:49113,133:_eb:61,61:1,-1:0,3:3,10:4,3:59,64:_eB:57969,36:1763,3:33,40:_eC:8073,0:190,0:48,0:7500,0:176,0:48,0:_eE:34870,24:-30,-24:199588,415:37,37:_eQ1:68,20:95,11:92,11:59,11:_eQ2:68,73:85,88:0,0:29,13:0,0:_CDP1vx:112850,247:113260,0:112850,247:113260:127506,248:128063:_CDP2vx:0,0:0,0:0,0:0:1,1:3:_f1:51,0:5,5:900,900,262,271,262,160:251,262,249,259,260,252,246,256,255:262,271,254,160,0,0,0,0,0,0:_g1:6,12:<LR>,<LI1>:11,0:0,0:<LI1>,<LD1>:G,G:_g2:1:1:G,G:2,1:2,1:0,0:0,0:_g3:1805,3:1276,3:,G:_h1:.:.:.:_i1:119:0,0:0,82:.

chr1    2494541 .   AG  A   6.183890    Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=119;NLODV=<NONE>;TNBQF=0,-68,0,0;TNCQF=0,0,0,0;tbDP=1812;tDP=1283;tAD=1276,4;t2DP=0;t2AD=0,0;RU=G;RC=6;R3X2=2494535,1,1,2494547,2,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aPositionL-53|cbDup-79:_A_:1283:1276,4:1812:1805,4:0:0,0:_Aa:2312,7,5,7,5,0,59,4,2110,0,0,0:24294,120,337758,12,7,5,700,500:_Ab:28,7,5,5:119719,814,285713,1486:102372,207765,7,5:_Ac:7,6:474,370,564,438:73,98,96,128:38,43,88,93:150,175,369,394:_AQ:136362,300:136962:50798,144:51062:28344,36:28453:_ADPf:770,1:773,0:444,0:445,0:_ADPr:692,3:696,0:368,1:370,0:_ALP:1154,1:1158:1010,1:1014:110978,126:111307:_ARP:1238,4:1246:1162,4:1170:188947,636:190066:_ALB:2009,5:1953,5:1961:443459,506:444794:_ARB:2009,5:1985,5:1995:798967,2787:803779:_ALI:519,0:457,0:457:812,1:815:_ARI:1333,4:1148,4:1153:1462,4:1469:_AX:2274,5:2284:227400,500:228400:2009,5:2019:2274,5:2284:_Ax:227400,500:119238,66:278777,721:2111,5:2236,5:_BDP:939,1:942,0:866,3:870,0:_BT:220737,198:221410:210704,632:211453:5069,23:5138:6490,92:6601:_CDP1:672,1:675,0:604,3:608,0:672,1:675,0:604,3:608,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:34,35:50624,143:28245,35:0,0:0,0:49113,118:_eb:61,61:1,-1:0,5:3,13:4,3:59,62:_eB:57969,37:1763,4:33,36:_eC:8073,0:190,0:48,0:7500,0:176,0:48,0:_eE:34870,10:-30,-20:199588,546:37,37:_eQ1:68,11:95,2:92,0:59,2:_eQ2:68,71:85,92:0,0:29,13:0,0:_CDP1vx:112850,163:113260,0:112850,163:113260:127506,309:128063:_CDP2vx:0,0:0,0:0,0:0:1,1:3:_f1:51,0:5,5:900,900,262,261,250,160:251,262,241,259,260,289,246,250,243:250,261,242,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:11,0:0,0:<LI1>,<LD1>:G,G:_g2:1:1:G,G:1,3:1,3:0,0:0,0:_g3:1805,4:1276,4:,G:_h1:.:.:.:_i1:119:0,0:0,82:.

chr1    2494541 .   A   C   6.183890    Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=112;NLODV=<NONE>;TNBQF=0,-62,0,0;TNCQF=0,0,0,0;tbDP=1820;tDP=1286;tAD=1276,9;t2DP=0;t2AD=0,0;RU=G;RC=6;R3X2=2494534,1,1,2494541,6,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aBQXM-23|aAlignR-58|bcDup-66:_A_:1286:1276,9:1820:1799,19:0:0,0:_Aa:2292,7,0,7,5,0,61,4,2014,0,0,0:24306,120,334770,12,7,0,700,0:_Ab:7,28,0,0:120620,814,281999,1466:99237,196979,6,5:_Ac:6,7:476,372,564,438:74,99,96,128:39,44,87,92:155,180,364,389:_AQ:134982,2280:137442:46755,340:47130:27754,23:27786:_ADPf:756,17:773,0:445,1:447,0:_ADPr:683,13:698,0:367,7:374,0:_ALP:913,6:919:793,6:799:91887,511:92398:_ARP:1168,0:1168:1109,0:1109:172273,369:172642:_ALB:1745,6:1696,6:1702:370291,2099:372390:_ARB:1745,6:1723,6:1729:710393,1440:711833:_ALI:516,4:429,4:433:812,8:821:_ARI:1316,23:1130,19:1151:1439,30:1471:_AX:2008,6:2014:201937,552:202566:1958,32:1993:2251,38:2292:_Ax:207075,748:120105,500:276296,5338:2038,34:2218,34:_BDP:933,11:944,0:866,8:876,0:_BT:218767,3168:221935:210528,2160:213253:5046,115:5161:6220,370:6670:_CDP1:672,4:676,0:604,5:610,0:624,1:625,0:562,0:562,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:33,11:47921,386:27963,27:204748,1648:218840,2733:41234,11:_eb:61,61:1,-1:0,2:3,9:5,3:59,74:_eB:48131,0:1419,0:35,0:_eC:7187,0:171,0:48,0:7216,0:170,0:48,0:_eE:42175,0:-42,-42:199494,1185:9,9:_eQ1:68,44:91,19:91,0:59,0:_eQ2:68,83:83,83:0,0:29,25:0,0:_CDP1vx:126272,505:126780,0:127081,1251:128335:127082,506:127689:_CDP2vx:0,0:0,0:0,0:0:1,1:3:_f1:51,0:40,40:900,900,177,197,215,160:168,241,169,177,201,177,177,177,169:215,197,205,160,0,0,0,0,0,0:_g1:0,1:A,C:0,0:0,0:T,C:,:_g2:.:.:.:.:.:.:.:_g3:1799,19:1276,9:,:_h1:.:.:.:_i1:112:0,0:84,0:.

[genetronhealth]

None of these variants is of high variant quality. We can filter based on QUAL (variant quality) and tAD (tumor allele depths).

The 6th column denotes QUAL. The variant quality of 11 and 6.183890 of a variant v mean that, on average, we can find one false positive variant that looks at least as real as v among 10^(11/10) and 10^(6.183890/10) genomic positions. Therefore, none of the variants is of high quality. tAD=1276,3 (1276,4 and 1276,9) means that there are 1276 REF reads and 3 (4 and 9) ALT reads at this locus. The ALT read support seems to be pretty low.

In general, if a variant has QUAL of at least 60, then this variant is highly likely to be true positive because if such variant is false positive then we are expected to find such variant among one million genomic positions.

[kokyriakidis]

Q1. What's the definition of false positives for uvc? False positives include also germline variants? As I said I want to detect indels. I do not care if they are somatic or germline. I care only about NOT being artifracts. DO you think I should stick with all variants with QUAL>60 or should I put a threshhold to let's say 50 or 40?

Q2. WIll uvc output variants which thinks they are germline?

Q3. Moreover, what is your opinion about these locations? Some variants have Q60 some Q50 on the same location. Both are correct??

chr1    27107650    .   T   TAA 6.16523 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=12;NLODV=<NONE>;TNBQF=0,-58,0,0;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,3;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:PASS:_A_:839:214,3:2020:721,9:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,600:135238:9181,106:28701:6802,159:22812:_ADPf:248,1:608,1:187,3:495,3:_ADPr:228,3:657,1:164,3:502,0:_ALP:368,6:1148:361,6:1086:49363,785:149301:_ARP:248,6:1108:241,4:1046:34125,682:145120:_ALB:432,10:425,10:1804:117041,2848:492775:_ARB:439,10:400,6:1758:104098,2110:476659:_ALI:302,5:253,5:675:351,6:997:_ARI:369,4:341,3:965:476,4:1265:_AX:776,10:2207:34160,780:133687:473,10:1866:827,10:2262:_Ax:49481,1000:91468,1872:108879,887:651,10:696,9:_BDP:378,4:976,3:343,5:1044,1:_BT:98915,1143:257828:89851,1334:279731:3042,125:19272:1733,115:20088:_CDP1:121,2:412,1:93,1:427,1:121,2:412,1:93,2:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,26:9044,104:6696,157:0,0:0,0:878,112:_eb:61,61:0,-1:0,0:3,9:10,7:61,70:_eB:8310,22:721,9:16,26:_eC:1436,5:47,1:40,32:821,0:33,0:36,0:_eE:801,19:0,22:31467,419:37,36:_eQ1:70,28:75,18:75,0:61,0:_eQ2:70,79:115,119:0,0:28,13:0,-22:_CDP1vx:16024,354:67720,38:16024,394:69134:21380,395:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,0:5,5:900,900,233,233,232,160:219,211,209,225,224,225,224,211,227:232,233,229,160,0,0,0,0,0,0:_g1:6,11:<LR>,<LI2>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:1:1:AA,AA:4,5:2,2:0,0:1,0:_g3:721,9:214,4:,AA:_h1:.:.:.:_i1:12:0,1:0,-25:.
chr1    27107650    .   TA  T   52  Q60 ANY_VAR;SomaticQ=12;TLODQ=52;NLODQ=12;NLODV=<NONE>;TNBQF=0,-6,0,52;TNCQF=0,-1,0,32;tbDP=2020;tDP=839;tAD=214,235;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-92:_A_:839:214,235:2020:721,550:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,36180:135238:9181,7198:28701:6802,5311:22812:_ADPf:248,160:608,1:187,116:495,3:_ADPr:228,187:657,1:164,140:502,0:_ALP:368,305:1148:361,286:1086:49363,40691:149301:_ARP:248,369:1108:241,355:1046:34125,47238:145120:_ALB:432,587:425,578:1804:117041,153250:492775:_ARB:439,603:400,574:1758:104098,160587:476659:_ALI:302,202:253,171:675:351,256:997:_ARI:369,304:341,280:965:476,347:1265:_AX:776,603:2207:34160,28777:133687:473,583:1866:827,603:2262:_Ax:49481,41286:91468,64836:108879,89018:651,603:696,557:_BDP:378,252:976,3:343,298:1044,1:_BT:98915,67530:257828:89851,80754:279731:3042,6679:19272:1733,7765:20088:_CDP1:121,108:412,1:93,127:427,1:121,115:412,1:93,133:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,20:9044,7000:6696,5164:0,0:0,0:878,1341:_eb:61,61:0,-1:0,1:3,10:10,6:61,87:_eB:8310,7892:721,550:16,20:_eC:1436,259:47,18:40,28:821,123:33,19:36,20:_eE:801,3210:0,47:31467,34662:37,37:_eQ1:70,76:75,67:75,52:61,59:_eQ2:70,96:115,138:0,32:28,12:0,-47:_CDP1vx:16024,22374:67720,38:16024,22853:69134:21380,22854:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,37:5,5:900,900,57,56,53,160:56,55,51,49,47,56,46,54,51:53,56,53,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:1:1:A,A:252,298:115,133:0,0:14,25:_g3:721,550:214,248:,A:_h1:((27107650&<LD1>)(27107671&<LD1>)&1&3)((27107647&<LD1>)(27107650&<LD1>)&4&0):((27107650&<LD1>)(27107668&<LD1>)&2&5&&2&5)((27107647&<LD1>)(27107650&<LD1>)&4&1&&4&3):.:_i1:12:0,1:0,-25:.
chr1    27107650    .   TAA T   48  Q50 ANY_VAR;SomaticQ=12;TLODQ=48;NLODQ=12;NLODV=<NONE>;TNBQF=0,-11,0,48;TNCQF=0,-1,0,17;tbDP=2020;tDP=839;tAD=214,197;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-78:_A_:839:214,197:2020:721,379:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,25140:135238:9181,5680:28701:6802,5535:22812:_ADPf:248,95:608,1:187,104:495,3:_ADPr:228,117:657,1:164,103:502,0:_ALP:368,237:1148:361,227:1086:49363,30474:149301:_ARP:248,240:1108:241,221:1046:34125,30890:145120:_ALB:432,406:425,403:1804:117041,114432:492775:_ARB:439,419:400,400:1758:104098,103560:476659:_ALI:302,170:253,144:675:351,207:997:_ARI:369,183:341,167:965:476,212:1265:_AX:776,419:2207:34160,33351:133687:473,404:1866:827,419:2262:_Ax:49481,41900:91468,51312:108879,54295:651,419:696,391:_BDP:378,175:976,3:343,204:1044,1:_BT:98915,46662:257828:89851,55978:279731:3042,4769:19272:1733,5255:20088:_CDP1:121,92:412,1:93,105:427,1:121,95:412,1:93,106:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,26:9044,5596:6696,5457:0,0:0,0:878,3541:_eb:61,61:0,-1:0,1:3,10:10,7:61,85:_eB:8310,7099:721,379:16,26:_eC:1436,242:47,14:40,32:821,3:33,5:36,20:_eE:801,2919:0,34:31467,28888:37,36:_eQ1:70,74:75,65:75,48:61,56:_eQ2:70,94:115,131:0,17:28,12:0,-34:_CDP1vx:16024,15552:67720,38:16024,15754:69134:21380,15755:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,32:5,5:900,900,73,73,62,160:68,53,61,65,63,67,65,61,71:62,73,61,160,0,0,0,0,0,0:_g1:6,8:<LR>,<LD2>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:1:1:AA,AA:175,204:95,106:0,0:9,6:_g3:721,379:214,201:,AA:_h1:((27107650&<LD2>)(27107950&<LD1>)&1&2)((27107650&<LD2>)(27107950&<LD2>)&2&1):((27107650&<LD2>)(27107950&<LD1>)&1&3&&1&3)((27107650&<LD2>)(27107671&<LD1>)&0&4)((27107650&<LD2>)(27107667&<LD1>)&1&2)((27107647&<LD1>)(27107650&<LD2>)&3&0):.:_i1:12:0,1:0,-25:.
chr1    27107650    .   TAAA    T   23  Q30 ANY_VAR;SomaticQ=12;TLODQ=23;NLODQ=12;NLODV=<NONE>;TNBQF=0,-24,0,23;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,144;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-68:_A_:839:214,144:2020:721,288:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,19033:135238:9181,5335:28701:6802,4134:22812:_ADPf:248,82:608,1:187,69:495,3:_ADPr:228,97:657,1:164,70:502,0:_ALP:368,191:1148:361,166:1086:49363,22645:149301:_ARP:248,197:1108:241,180:1046:34125,25752:145120:_ALB:432,314:425,310:1804:117041,85104:492775:_ARB:439,318:400,300:1758:104098,84896:476659:_ALI:302,112:253,79:675:351,139:997:_ARI:369,162:341,144:965:476,179:1265:_AX:776,318:2207:34160,30554:133687:473,313:1866:827,318:2262:_Ax:49481,31800:91468,34918:108879,44950:651,318:696,305:_BDP:378,134:976,3:343,154:1044,1:_BT:98915,35552:257828:89851,41687:279731:3042,3794:19272:1733,4188:20088:_CDP1:121,67:412,1:93,77:427,1:121,67:412,1:93,77:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,29:9044,5319:6696,4121:0,0:0,0:878,3744:_eb:61,61:0,0:0,1:3,10:10,7:61,84:_eB:8310,5627:721,288:16,28:_eC:1436,537:47,20:40,40:821,481:33,21:36,36:_eE:801,1156:0,28:31467,20906:37,35:_eQ1:70,63:75,54:75,23:61,11:_eQ2:70,93:115,129:0,0:28,22:0,-28:_CDP1vx:16024,5874:67720,38:16024,5874:69134:21380,5875:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,19:5,5:900,900,85,115,99,160:85,63,78,76,75,76,73,80,78:99,115,74,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:4:4:AAA,AAAAA,AAAAAA,AAAA,AAA,AAAAA,AAAA,AAAAAA:61,46,15,12,80,37,33,4:39,14,9,5,47,16,13,1:0,0,0,0,0,0,0,0:2,8,2,1,2,7,5,0:_g3:721,141:214,86:,AAA:_h1:((27107650&<LD3P>)(27107950&<LD2>)&6&3&&6&3)((27107650&<LD3P>)(27107671&<LD1>)&1&7&&1&8)((27107650&<LD3P>)(27107950&<LD1>)&1&4&&2&4)((27107209&T)(27107650&<LD3P>)&3&0):((27107650&<LD3P>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:12:0,1:0,-25:.
chr1    27107650    .   TAAAAA  T   6.16523 Q10 ANY_VAR;SomaticQ=-17;TLODQ=-17;NLODQ=12;NLODV=<NONE>;TNBQF=0,-33,0,1;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,144;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-68|bcDup-87:_A_:839:214,144:2020:721,288:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,19033:135238:9181,5335:28701:6802,4134:22812:_ADPf:248,82:608,1:187,69:495,3:_ADPr:228,97:657,1:164,70:502,0:_ALP:368,191:1148:361,166:1086:49363,22645:149301:_ARP:248,197:1108:241,180:1046:34125,25752:145120:_ALB:432,314:425,310:1804:117041,85104:492775:_ARB:439,318:400,300:1758:104098,84896:476659:_ALI:302,112:253,79:675:351,139:997:_ARI:369,162:341,144:965:476,179:1265:_AX:776,318:2207:34160,30554:133687:473,313:1866:827,318:2262:_Ax:49481,31800:91468,34918:108879,44950:651,318:696,305:_BDP:378,134:976,3:343,154:1044,1:_BT:98915,35552:257828:89851,41687:279731:3042,3794:19272:1733,4188:20088:_CDP1:121,67:412,1:93,77:427,1:121,67:412,1:93,77:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,29:9044,5319:6696,4121:0,0:0,0:878,3744:_eb:61,61:0,0:0,1:3,10:10,7:61,84:_eB:8310,5627:721,288:16,28:_eC:1436,537:47,20:40,40:821,481:33,21:36,36:_eE:801,596:0,18:31467,20904:37,33:_eQ1:70,58:75,48:75,1:61,0:_eQ2:70,93:115,123:0,0:28,22:0,-18:_CDP1vx:16024,3001:67720,38:16024,3466:69134:21380,3002:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,10:5,5:900,900,85,115,99,160,900,900,85,138,145,160:85,63,78,76,75,76,73,80,78,85,63,78,76,75,76,73,80,78:99,115,74,160,0,0,0,0,0,0,145,138,74,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:4:4:AAA,AAAAA,AAAAAA,AAAA,AAA,AAAAA,AAAA,AAAAAA:61,46,15,12,80,37,33,4:39,14,9,5,47,16,13,1:0,0,0,0,0,0,0,0:2,8,2,1,2,7,5,0:_g3:721,83:214,30:,AAAAA:_h1:((27107650&<LD3P>)(27107950&<LD2>)&6&3&&6&3)((27107650&<LD3P>)(27107671&<LD1>)&1&7&&1&8)((27107650&<LD3P>)(27107950&<LD1>)&1&4&&2&4)((27107209&T)(27107650&<LD3P>)&3&0):((27107650&<LD3P>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:12:0,1:0,-25:.
chr1    27107650    .   TAAAA   T   6.16523 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=12;NLODV=<NONE>;TNBQF=0,-39,0,0;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,144;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-68|bcDup-87:_A_:839:214,144:2020:721,288:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,19033:135238:9181,5335:28701:6802,4134:22812:_ADPf:248,82:608,1:187,69:495,3:_ADPr:228,97:657,1:164,70:502,0:_ALP:368,191:1148:361,166:1086:49363,22645:149301:_ARP:248,197:1108:241,180:1046:34125,25752:145120:_ALB:432,314:425,310:1804:117041,85104:492775:_ARB:439,318:400,300:1758:104098,84896:476659:_ALI:302,112:253,79:675:351,139:997:_ARI:369,162:341,144:965:476,179:1265:_AX:776,318:2207:34160,30554:133687:473,313:1866:827,318:2262:_Ax:49481,31800:91468,34918:108879,44950:651,318:696,305:_BDP:378,134:976,3:343,154:1044,1:_BT:98915,35552:257828:89851,41687:279731:3042,3794:19272:1733,4188:20088:_CDP1:121,67:412,1:93,77:427,1:121,67:412,1:93,77:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,29:9044,5319:6696,4121:0,0:0,0:878,3744:_eb:61,61:0,0:0,1:3,10:10,7:61,84:_eB:8310,5627:721,288:16,28:_eC:1436,537:47,20:40,40:821,481:33,21:36,36:_eE:801,362:0,23:31467,20905:37,34:_eQ1:70,50:75,40:75,0:61,0:_eQ2:70,93:115,126:0,0:28,22:0,-23:_CDP1vx:16024,1802:67720,38:16024,1888:69134:21380,1803:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,4:5,5:900,900,85,115,99,160,900,900,85,138,145,160,900,900,85,165,167,160:85,63,78,76,75,76,73,80,78,85,63,78,76,75,76,73,80,78,85,63,78,76,75,76,73,80,78:99,115,74,160,0,0,0,0,0,0,145,138,74,160,0,0,0,0,0,0,167,165,74,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:4:4:AAA,AAAAA,AAAAAA,AAAA,AAA,AAAAA,AAAA,AAAAAA:61,46,15,12,80,37,33,4:39,14,9,5,47,16,13,1:0,0,0,0,0,0,0,0:2,8,2,1,2,7,5,0:_g3:721,45:214,18:,AAAA:_h1:((27107650&<LD3P>)(27107950&<LD2>)&6&3&&6&3)((27107650&<LD3P>)(27107671&<LD1>)&1&7&&1&8)((27107650&<LD3P>)(27107950&<LD1>)&1&4&&2&4)((27107209&T)(27107650&<LD3P>)&3&0):((27107650&<LD3P>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:12:0,1:0,-25:.
chr1    27107667    .   AAT A   6.18389 Q10 ANY_VAR;SomaticQ=-14;TLODQ=-14;NLODQ=130;NLODV=<NONE>;TNBQF=0,-72,0,0;TNCQF=0,0,0,2;tbDP=2153;tDP=875;tAD=861,10;t2DP=0;t2AD=0,0;RU=A;RC=1;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aBQXM-32|aPositionR-56|cbDup-42:_A_:875:861,10:2153:2139,10:0:0,0:_Aa:2413,1,20,99,1428,0,65,1,2204,0,0,0:42445,14436,357480,2896,1,164,100,805:_Ab:4,1,117,339:260649,993,350808,1367:159437,170475,97,2599:_Ac:8,9:704,543,693,534:131,175,128,171:62,67,67,72:171,196,260,285:_AQ:141329,597:142166:27800,82:27917:20599,0:20599:_ADPf:625,3:631,2:487,0:487,0:_ADPr:731,7:739,1:524,0:524,0:_ALP:1088,6:1094:1044,5:1049:135262,717:136008:_ARP:1007,2:1010:970,2:973:134005,439:134566:_ALB:1605,10:1565,9:1575:426314,2151:428515:_ARB:1557,10:1467,8:1476:416463,1612:418588:_ALI:828,0:680,0:680:1011,0:1011:_ARI:1162,8:1036,8:1047:1356,10:1370:_AX:2085,10:2096:110185,76:110297:1853,10:1867:2367,10:2381:_Ax:157664,106:260557,0:337947,2443:1951,10:2096,4:_BDP:995,3:1001,2:1144,7:1152,1:_BT:262451,662:263844:308810,1746:310839:19514,92:19675:20494,207:20724:_CDP1:418,3:424,2:443,7:451,1:418,3:424,2:443,7:451,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,7:27120,77:20093,0:0,0:0,0:16007,7:_eb:61,61:0,0:0,2:7,12:8,7:60,68:_eB:36302,0:2139,0:17,0:_eC:11927,0:260,0:48,0:12810,0:279,0:48,0:_eE:6408,-8:0,4:134502,1364:37,36:_eQ1:69,23:91,6:91,0:60,0:_eQ2:69,77:115,125:0,2:38,13:0,-4:_CDP1vx:57218,123:57342,1:57218,215:57434:86007,124:86193:_CDP2vx:0,0:0,0:0,0:0:1,1:3:_f1:51,0:5,5:900,900,236,231,194,160:212,285,209,220,217,224,261,226,210:194,231,194,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:0,0:2,0:<LD1>,*:AT,:_g2:1:1:AT,AT:3,7:3,7:0,0:0,0:_g3:2139,10:861,10:,AT:_h1:.:((27107650&<LD2>)(27107667&<LD1>)&1&2):.:_i1:130:0,0:0,93:.
chr1    27107668    .   AT  A   6.18071 Q10 ANY_VAR;SomaticQ=-14;TLODQ=-14;NLODQ=130;NLODV=<NONE>;TNBQF=0,-52,0,0;TNCQF=0,0,0,2;tbDP=2154;tDP=867;tAD=831,24;t2DP=0;t2AD=0,0;RU=T;RC=1;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aBQXM-92|aPositionR-57|cbDup-41:_A_:867:831,24:2154:2117,24:0:0,0:_Aa:2425,0,38,98,1428,0,49,3,2126,0,1,0:42039,14426,359195,2892,0,182,0,2605:_Ab:0,0,237,219:257496,986,359891,1389:153854,164637,89,2527:_Ac:8,8:702,541,698,538:130,174,129,173:62,67,67,72:175,200,259,284:_AQ:139769,1500:142046:29135,272:29512:21135,172:21307:_ADPf:613,8:626,5:471,5:476,0:_ADPr:740,12:760,8:517,0:517,0:_ALP:1083,20:1103:1049,20:1069:136101,2279:138380:_ARP:1029,6:1035:987,6:993:135873,1168:137041:_ALB:1538,23:1513,23:1536:397927,6725:404652:_ARB:1499,18:1456,18:1474:412578,4193:416771:_ALI:814,4:672,4:676:988,5:993:_ARI:1162,17:1037,15:1062:1353,20:1386:_AX:2074,25:2099:118818,1023:119937:1793,24:1830:2341,25:2379:_Ax:172116,1130:254262,1729:340628,4263:1952,25:2087,16:_BDP:971,12:988,5:1146,12:1166,8:_BT:256617,2978:260687:309418,3266:314713:18887,467:19492:20180,364:20774:_CDP1:399,12:416,5:432,12:451,7:399,12:416,5:432,12:451,7:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:21,21:28955,335:21005,171:0,0:0,0:18596,99:_eb:61,61:0,-1:0,2:7,13:10,7:60,72:_eB:37946,5:2117,8:18,25:_eC:11396,0:249,0:48,0:12558,0:274,0:48,0:_eE:6555,-5:0,7:129468,3317:37,37:_eQ1:69,32:91,23:91,0:60,0:_eQ2:69,81:115,122:0,2:38,13:0,-7:_CDP1vx:54628,527:55420,4:54628,527:55420:83010,745:84150:_CDP2vx:0,0:0,0:0,0:0:1,1:4:_f1:51,0:5,5:900,900,197,207,168,160:183,201,178,182,191,173,222,193,179:168,207,152,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:0,0:2,0:<LD1>,*:T,:_g2:2:1:TAC,T,T:6,6,12:6,6,12:0,0,0:0,0,0:_g3:2117,18:831,18:,T:_h1:.:((27107650&<LD1>)(27107668&<LD1>)&2&5&&2&5):.:_i1:130:0,0:0,93:.
chr1    27107668    .   ATAC    A   6.18071 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=130;NLODV=<NONE>;TNBQF=0,-64,0,0;TNCQF=0,0,0,0;tbDP=2154;tDP=867;tAD=831,24;t2DP=0;t2AD=0,0;RU=T;RC=1;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aBQXM-92|aPositionR-57|cbDup-41|aBQXM-92|aPositionR-57|cbDup-43:_A_:867:831,24:2154:2117,24:0:0,0:_Aa:2425,0,38,98,1428,0,49,3,2126,0,1,0:42039,14426,359195,2892,0,182,0,2605:_Ab:0,0,237,219:257496,986,359891,1389:153854,164637,89,2527:_Ac:8,8:702,541,698,538:130,174,129,173:62,67,67,72:175,200,259,284:_AQ:139769,1500:142046:29135,272:29512:21135,172:21307:_ADPf:613,8:626,5:471,5:476,0:_ADPr:740,12:760,8:517,0:517,0:_ALP:1083,20:1103:1049,20:1069:136101,2279:138380:_ARP:1029,6:1035:987,6:993:135873,1168:137041:_ALB:1538,23:1513,23:1536:397927,6725:404652:_ARB:1499,18:1456,18:1474:412578,4193:416771:_ALI:814,4:672,4:676:988,5:993:_ARI:1162,17:1037,15:1062:1353,20:1386:_AX:2074,25:2099:118818,1023:119937:1793,24:1830:2341,25:2379:_Ax:172116,1130:254262,1729:340628,4263:1952,25:2087,16:_BDP:971,12:988,5:1146,12:1166,8:_BT:256617,2978:260687:309418,3266:314713:18887,467:19492:20180,364:20774:_CDP1:399,12:416,5:432,12:451,7:399,12:416,5:432,12:451,7:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:21,21:28955,335:21005,171:0,0:0,0:18596,99:_eb:61,61:0,-1:0,2:7,13:10,7:60,72:_eB:37946,5:2117,8:18,25:_eC:11396,0:249,0:48,0:12558,0:274,0:48,0:_eE:6555,-7:0,1:129468,3315:37,35:_eQ1:69,27:91,18:91,0:60,0:_eQ2:69,81:115,126:0,0:38,13:0,-1:_CDP1vx:54628,261:55420,4:54628,261:55420:83010,262:84150:_CDP2vx:0,0:0,0:0,0:0:1,1:4:_f1:51,0:5,5:900,900,197,207,168,160,900,900,197,252,216,160:183,201,178,182,191,173,222,193,179,183,201,178,182,191,173,222,193,179:168,207,152,160,0,0,0,0,0,0,216,252,152,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:0,0:2,0:<LD1>,*:T,:_g2:2:1:TAC,T,T:6,6,12:6,6,12:0,0,0:0,0,0:_g3:2117,6:831,6:,TAC:_h1:.:((27107650&<LD1>)(27107668&<LD1>)&2&5&&2&5):.:_i1:130:0,0:0,93:.
chr1    27107671    .   CA  C   20  Q30 ANY_VAR;SomaticQ=20;TLODQ=20;NLODQ=114;NLODV=<NONE>;TNBQF=0,-53,0,14;TNCQF=0,0,0,20;tbDP=2235;tDP=891;tAD=868,14;t2DP=0;t2AD=0,0;RU=A;RC=9;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aPositionR-64|cbDup-53:_A_:891:868,14:2235:2208,18:0:0,0:_Aa:2484,2,27,97,1423,0,102,4,2370,0,0,0:42622,14370,368058,2886,2,118,200,2147:_Ab:8,2,294,35:258728,991,372001,1442:170323,184330,106,2695:_Ac:9,6:702,541,695,536:130,174,128,172:61,66,67,72:174,199,263,288:_AQ:145946,1140:147626:39944,238:40266:27146,182:27517:_ADPf:663,3:670,3:477,0:482,5:_ADPr:789,9:798,0:514,7:522,0:_ALP:1093,16:1116:1042,16:1064:136913,1843:139693:_ARP:1062,5:1068:994,4:999:138202,955:139308:_ALB:1632,18:1466,18:1486:389362,5980:395710:_ARB:1732,18:1706,17:1724:548017,3565:551978:_ALI:827,6:682,3:689:991,7:1004:_ARI:1256,11:1112,4:1117:1452,12:1468:_AX:2159,19:2186:204829,1138:206706:1985,18:2007:2443,19:2472:_Ax:242924,1534:254429,1507:367649,2695:1988,19:2174,19:_BDP:1019,3:1030,7:1189,15:1205,0:_BT:268434,868:271101:320641,3793:324502:19172,106:19635:20282,705:21032:_CDP1:415,3:426,7:453,11:465,0:415,3:426,7:453,11:465,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:27,23:39552,256:26885,181:0,0:0,0:33995,127:_eb:61,61:-2,-1:0,5:7,17:11,7:60,67:_eB:52875,39:2208,12:24,26:_eC:12223,0:266,0:48,0:13425,9:292,1:48,36:_eE:10705,16:0,22:135446,1916:37,37:_eQ1:69,27:92,18:92,14:60,16:_eQ2:69,76:115,125:0,20:39,14:0,-22:_CDP1vx:58822,449:59342,3:58822,449:59361:86708,682:87764:_CDP2vx:0,0:0,0:0,0:0:1,1:4:_f1:51,0:5,5:900,900,210,208,180,160:207,212,199,192,198,182,230,204,200:180,208,179,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:14,0:20,3:<LD1>,<LI1>:A,A:_g2:1:1:A,A:3,15:3,11:0,0:0,1:_g3:2208,18:868,14:,A:_h1:((27107650&<LD3P>)(27107671&<LD1>)&1&7)((27107650&<LD1>)(27107671&<LD1>)&1&3):((27107650&<LD2>)(27107671&<LD1>)&0&4)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:114:0,0:0,77:.
chr1    27107950    .   G   GA  26  Q30 ANY_VAR;SomaticQ=26;TLODQ=26;NLODQ=27;NLODV=<NONE>;TNBQF=0,-40,0,26;TNCQF=0,-1,0,5;tbDP=3538;tDP=974;tAD=590,47;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-49:_A_:974:590,47:3538:2686,69:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,4620:248619:42396,1284:57940:29303,696:38757:_ADPf:934,17:1233,1:612,12:782,4:_ADPr:934,31:1240,0:676,17:890,2:_ALP:1513,35:2007:1443,34:1900:184782,4376:241910:_ARP:1642,51:2221:1586,51:2137:233494,6836:315229:_ALB:2711,76:2635,76:3542:597346,15496:801090:_ARB:2727,77:2679,76:3644:853912,24777:1178870:_ALI:970,23:895,21:1145:1288,29:1672:_ARI:1663,44:1308,24:1702:1868,48:2473:_AX:3145,77:4127:178934,5886:249376:2680,76:3604:3156,77:4145:_Ax:259035,6907:260944,5263:456654,10290:2981,77:3012,73:_BDP:1344,28:1761,2:1342,41:1777,2:_BT:358749,7511:466549:350428,9780:460981:4459,657:15370:5389,975:16545:_CDP1:299,20:493,2:291,27:481,1:299,16:493,2:291,23:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,25:41727,1284:28829,711:0,0:0,0:17895,641:_eb:61,61:1,-1:0,2:1,9:10,3:58,74:_eB:51155,557:2497,60:22,27:_eC:9058,0:205,0:48,0:9372,1:211,1:48,28:_eE:8311,161:0,17:89556,6576:37,37:_eQ1:67,48:90,38:90,26:58,0:_eQ2:67,83:115,114:0,5:39,12:0,-17:_CDP1vx:58944,1683:81457,1:63703,1810:86909:58945,1913:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,0:5,5:900,900,173,171,140,160:171,156,159,167,168,173,162,169,159:140,171,124,160,0,0,0,0,0,0:_g1:6,12:<LR>,<LI1>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:1:1:A,A:28,41:16,23:0,0:0,2:_g3:2686,69:590,39:,A:_h1:.:.:.:_i1:27:0,1:0,-10:.
chr1    27107950    .   GA  G   49  Q50 ANY_VAR;SomaticQ=27;TLODQ=49;NLODQ=27;NLODV=<NONE>;TNBQF=0,-16,0,49;TNCQF=0,-1,0,22;tbDP=3538;tDP=974;tAD=590,200;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-58:_A_:974:590,200:3538:2686,436:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,30240:248619:42396,6202:57940:29303,4331:38757:_ADPf:934,138:1233,1:612,95:782,4:_ADPr:934,159:1240,0:676,112:890,2:_ALP:1513,246:2007:1443,233:1900:184782,28933:241910:_ARP:1642,285:2221:1586,270:2137:233494,40854:315229:_ALB:2711,468:2635,454:3542:597346,103293:801090:_ARB:2727,504:2679,495:3644:853912,166541:1178870:_ALI:970,155:895,140:1145:1288,207:1672:_ARI:1663,265:1308,197:1702:1868,297:2473:_AX:3145,504:4127:178934,24441:249376:2680,463:3604:3156,504:4145:_Ax:259035,34974:260944,39977:456654,67898:2981,504:3012,492:_BDP:1344,206:1761,2:1342,230:1777,2:_BT:358749,53199:466549:350428,59005:460981:4459,5292:15370:5389,5798:16545:_CDP1:299,99:493,2:291,101:481,1:299,103:493,2:291,105:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,20:41727,6028:28829,4206:0,0:0,0:17895,1188:_eb:61,61:1,-1:0,3:1,10:10,3:58,81:_eB:51155,4755:2497,436:22,20:_eC:9058,476:205,25:48,32:9372,418:211,27:48,28:_eE:8311,1298:0,32:89556,29196:37,37:_eQ1:67,68:90,59:90,49:58,59:_eQ2:67,90:115,129:0,22:39,17:0,-32:_CDP1vx:58944,11851:81457,1:63703,12013:86909:58945,12014:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,26:5,5:900,900,91,91,67,160:91,87,82,88,86,89,88,87,82:67,91,68,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:1:1:A,A:206,230:103,105:0,0:19,24:_g3:2686,436:590,208:,A:_h1:((27107859&T)(27107950&<LD1>)&8&7&&8&7)((27107950&<LD1>)(27108179&A)&8&4&&9&4)((27107650&<LD3P>)(27107950&<LD1>)&1&4)((27107949&<LD1>)(27107950&<LD1>)&3&0)((27107650&<LD2>)(27107950&<LD1>)&1&2):((27107859&T)(27107950&<LD1>)&3&3&&3&3)((27107950&<LD1>)(27108179&A)&3&1)((27107650&<LD2>)(27107950&<LD1>)&1&3)((27107949&<LD1>)(27107950&<LD1>)&3&0):((27107859&T)(27107950&<LD1>)&2&3&&2&3)((27107950&<LD1>)(27108179&A)&2&1&&2&1):_i1:27:0,1:0,-10:.
chr1    27107950    .   GAA G   41  Q50 ANY_VAR;SomaticQ=27;TLODQ=41;NLODQ=27;NLODV=<NONE>;TNBQF=0,-20,0,41;TNCQF=0,-1,0,8;tbDP=3538;tDP=974;tAD=590,122;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-72:_A_:974:590,122:3538:2686,317:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,22260:248619:42396,7357:57940:29303,4107:38757:_ADPf:934,135:1233,1:612,54:782,4:_ADPr:934,103:1240,0:676,79:890,2:_ALP:1513,193:2007:1443,171:1900:184782,21637:241910:_ARP:1642,226:2221:1586,213:2137:233494,31601:315229:_ALB:2711,356:2635,348:3542:597346,77265:801090:_ARB:2727,371:2679,364:3644:853912,125175:1178870:_ALI:970,85:895,79:1145:1288,133:1672:_ARI:1663,226:1308,163:1702:1868,238:2473:_AX:3145,371:4127:178934,37093:249376:2680,348:3604:3156,371:4145:_Ax:259035,37100:260944,22165:456654,54769:2981,371:3012,366:_BDP:1344,169:1761,2:1342,148:1777,2:_BT:358749,43175:466549:350428,37692:460981:4459,4571:15370:5389,3909:16545:_CDP1:299,67:493,2:291,55:481,1:299,67:493,2:291,55:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,30:41727,7351:28829,4103:0,0:0,0:17895,4805:_eb:61,61:1,-1:0,3:1,10:10,3:58,80:_eB:51155,6188:2497,317:22,30:_eC:9058,707:205,26:48,40:9372,497:211,22:48,36:_eE:8311,1635:0,24:89556,17537:37,36:_eQ1:67,67:90,57:90,41:58,50:_eQ2:67,89:115,127:0,8:39,22:0,-24:_CDP1vx:58944,8350:81457,1:63703,8738:86909:58945,8739:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,21:5,5:900,900,105,105,90,160:102,83,89,100,99,100,98,107,89:90,105,86,160,0,0,0,0,0,0:_g1:6,8:<LR>,<LD2>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:1:1:AA,AA:169,148:67,55:0,0:21,17:_g3:2686,317:590,122:,AA:_h1:((27107859&T)(27107950&<LD2>)&7&5&&7&5)((27107650&<LD3P>)(27107950&<LD2>)&6&3)((27107950&<LD2>)(27108262&A)&5&3)((27107950&<LD2>)(27108179&A)&4&3):((27107859&T)(27107950&<LD2>)&4&2&&4&2)((27107947&<LD1>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107950&<LD2>)&2&2):((27107859&T)(27107950&<LD2>)&2&2&&2&2):_i1:27:0,1:0,-10:.
chr1    27107950    .   GAAA    G   6.17133 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=27;NLODV=<NONE>;TNBQF=0,-55,0,0;TNCQF=0,-1,0,0;tbDP=3538;tDP=974;tAD=590,10;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-53:_A_:974:590,10:3538:2686,21:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,1500:248619:42396,596:57940:29303,231:38757:_ADPf:934,8:1233,1:612,3:782,4:_ADPr:934,10:1240,0:676,4:890,2:_ALP:1513,16:2007:1443,15:1900:184782,1889:241910:_ARP:1642,13:2221:1586,13:2137:233494,1988:315229:_ALB:2711,25:2635,24:3542:597346,6693:801090:_ARB:2727,25:2679,25:3644:853912,6881:1178870:_ALI:970,6:895,5:1145:1288,7:1672:_ARI:1663,16:1308,9:1702:1868,18:2473:_AX:3145,25:4127:178934,2500:249376:2680,25:3604:3156,25:4145:_Ax:259035,2500:260944,1113:456654,3233:2981,25:3012,25:_BDP:1344,10:1761,2:1342,11:1777,2:_BT:358749,2714:466549:350428,2840:460981:4459,253:15370:5389,317:16545:_CDP1:299,4:493,2:291,6:481,1:299,4:493,2:291,6:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,33:41727,595:28829,230:0,0:0,0:17895,406:_eb:61,61:1,-1:0,3:1,10:10,3:58,68:_eB:51155,225:2497,21:22,33:_eC:9058,0:205,0:48,0:9372,0:211,0:48,0:_eE:8311,64:0,15:89556,1358:37,35:_eQ1:67,32:90,23:90,0:58,0:_eQ2:67,77:115,122:0,0:39,9:0,-15:_CDP1vx:58944,536:81457,1:63703,536:86909:58945,537:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,0:5,5:900,900,221,226,199,160:213,199,202,215,216,207,221,215,202:199,226,187,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:2:1:AAA,AAAA,AAA:8,2,11:4,0,6:0,0,0:0,0,1:_g3:2686,19:590,10:,AAA:_h1:.:.:.:_i1:27:0,1:0,-10:.

Q4. I have a truth set and saw that a lot of TRUE indels have Q50 with some of them having quality 40 (so they are borderline Q50). I guess the cut-off for tumor-only sample should be set to Q50. If I include Q40 variants, it adds 248 more INDELS. I guess most of them will be FPs.

[genetronhealth]

Hi @kokyriakidis

Thank you for your interest in UVC-delins. Here are my answers to all your above questions.

Q1:

What's the definition of false positives for uvc? False positives include also germline variants?

The definition of false positive depends on the calling mode of UVC. UVC has two calling modes: somatic-only mode (with VCF result line denoted by the SOMATIC tag in the INFO column and generated by running the script uvcTN.sh) and both-germline-and-somatic mode (with VCF result line denoted by the ANY_VAR tag in the INFO column and generated by running uvc1 and similar binary executable files, and not generated by running uvcTN.sh). In the somatic-only calling mode. false positive means not somatic. In the both-germline-and-somatic calling mode, false positive means neither germline nor somatic.

As I said I want to detect indels. I do not care if they are somatic or germline. I care only about NOT being artifracts. DO you think I should stick with all variants with QUAL>60 or should I put a threshhold to let's say 50 or 40?

"QUAL>=60" is good for most purposes. In general, >=60 is for detecting any mutation (>=50 can be used for more sensitivity especially for tumor-only sample), >=40 is for detecting hotspot mutation (such as these in the COSMIC database with CNT of at least 5, and >=30 can be used to get more sensitivity especially for tumor-only sample), and >=20 is for detecting extremely important hotspot mutations (such as EGFR exon 19 deletion).

Q2:

WIll uvc output variants which thinks they are germline?

As mentioned above, uvc1 and similar binary executable files will output variants of germline origin. The script uvcTN.sh will either not output variants of germline origin or give low variant quality (QUAL) to germline variants in the resulting VCF file. In brief, uvc1 is for calling variants of any origin and uvcTN.sh is for calling variants of only somatic origin.

Q3.

Moreover, what is your opinion about these locations?

v1  chr1    27107650    .   T   TAA 6.16523 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=12;NLODV=<NONE>;TNBQF=0,-58,0,0;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,3;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:PASS:_A_:839:214,3:2020:721,9:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,600:135238:9181,106:28701:6802,159:22812:_ADPf:248,1:608,1:187,3:495,3:_ADPr:228,3:657,1:164,3:502,0:_ALP:368,6:1148:361,6:1086:49363,785:149301:_ARP:248,6:1108:241,4:1046:34125,682:145120:_ALB:432,10:425,10:1804:117041,2848:492775:_ARB:439,10:400,6:1758:104098,2110:476659:_ALI:302,5:253,5:675:351,6:997:_ARI:369,4:341,3:965:476,4:1265:_AX:776,10:2207:34160,780:133687:473,10:1866:827,10:2262:_Ax:49481,1000:91468,1872:108879,887:651,10:696,9:_BDP:378,4:976,3:343,5:1044,1:_BT:98915,1143:257828:89851,1334:279731:3042,125:19272:1733,115:20088:_CDP1:121,2:412,1:93,1:427,1:121,2:412,1:93,2:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,26:9044,104:6696,157:0,0:0,0:878,112:_eb:61,61:0,-1:0,0:3,9:10,7:61,70:_eB:8310,22:721,9:16,26:_eC:1436,5:47,1:40,32:821,0:33,0:36,0:_eE:801,19:0,22:31467,419:37,36:_eQ1:70,28:75,18:75,0:61,0:_eQ2:70,79:115,119:0,0:28,13:0,-22:_CDP1vx:16024,354:67720,38:16024,394:69134:21380,395:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,0:5,5:900,900,233,233,232,160:219,211,209,225,224,225,224,211,227:232,233,229,160,0,0,0,0,0,0:_g1:6,11:<LR>,<LI2>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:1:1:AA,AA:4,5:2,2:0,0:1,0:_g3:721,9:214,4:,AA:_h1:.:.:.:_i1:12:0,1:0,-25:.
v2  chr1    27107650    .   TA  T   52  Q60 ANY_VAR;SomaticQ=12;TLODQ=52;NLODQ=12;NLODV=<NONE>;TNBQF=0,-6,0,52;TNCQF=0,-1,0,32;tbDP=2020;tDP=839;tAD=214,235;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-92:_A_:839:214,235:2020:721,550:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,36180:135238:9181,7198:28701:6802,5311:22812:_ADPf:248,160:608,1:187,116:495,3:_ADPr:228,187:657,1:164,140:502,0:_ALP:368,305:1148:361,286:1086:49363,40691:149301:_ARP:248,369:1108:241,355:1046:34125,47238:145120:_ALB:432,587:425,578:1804:117041,153250:492775:_ARB:439,603:400,574:1758:104098,160587:476659:_ALI:302,202:253,171:675:351,256:997:_ARI:369,304:341,280:965:476,347:1265:_AX:776,603:2207:34160,28777:133687:473,583:1866:827,603:2262:_Ax:49481,41286:91468,64836:108879,89018:651,603:696,557:_BDP:378,252:976,3:343,298:1044,1:_BT:98915,67530:257828:89851,80754:279731:3042,6679:19272:1733,7765:20088:_CDP1:121,108:412,1:93,127:427,1:121,115:412,1:93,133:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,20:9044,7000:6696,5164:0,0:0,0:878,1341:_eb:61,61:0,-1:0,1:3,10:10,6:61,87:_eB:8310,7892:721,550:16,20:_eC:1436,259:47,18:40,28:821,123:33,19:36,20:_eE:801,3210:0,47:31467,34662:37,37:_eQ1:70,76:75,67:75,52:61,59:_eQ2:70,96:115,138:0,32:28,12:0,-47:_CDP1vx:16024,22374:67720,38:16024,22853:69134:21380,22854:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,37:5,5:900,900,57,56,53,160:56,55,51,49,47,56,46,54,51:53,56,53,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:1:1:A,A:252,298:115,133:0,0:14,25:_g3:721,550:214,248:,A:_h1:((27107650&<LD1>)(27107671&<LD1>)&1&3)((27107647&<LD1>)(27107650&<LD1>)&4&0):((27107650&<LD1>)(27107668&<LD1>)&2&5&&2&5)((27107647&<LD1>)(27107650&<LD1>)&4&1&&4&3):.:_i1:12:0,1:0,-25:.
v3  chr1    27107650    .   TAA T   48  Q50 ANY_VAR;SomaticQ=12;TLODQ=48;NLODQ=12;NLODV=<NONE>;TNBQF=0,-11,0,48;TNCQF=0,-1,0,17;tbDP=2020;tDP=839;tAD=214,197;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-78:_A_:839:214,197:2020:721,379:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,25140:135238:9181,5680:28701:6802,5535:22812:_ADPf:248,95:608,1:187,104:495,3:_ADPr:228,117:657,1:164,103:502,0:_ALP:368,237:1148:361,227:1086:49363,30474:149301:_ARP:248,240:1108:241,221:1046:34125,30890:145120:_ALB:432,406:425,403:1804:117041,114432:492775:_ARB:439,419:400,400:1758:104098,103560:476659:_ALI:302,170:253,144:675:351,207:997:_ARI:369,183:341,167:965:476,212:1265:_AX:776,419:2207:34160,33351:133687:473,404:1866:827,419:2262:_Ax:49481,41900:91468,51312:108879,54295:651,419:696,391:_BDP:378,175:976,3:343,204:1044,1:_BT:98915,46662:257828:89851,55978:279731:3042,4769:19272:1733,5255:20088:_CDP1:121,92:412,1:93,105:427,1:121,95:412,1:93,106:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,26:9044,5596:6696,5457:0,0:0,0:878,3541:_eb:61,61:0,-1:0,1:3,10:10,7:61,85:_eB:8310,7099:721,379:16,26:_eC:1436,242:47,14:40,32:821,3:33,5:36,20:_eE:801,2919:0,34:31467,28888:37,36:_eQ1:70,74:75,65:75,48:61,56:_eQ2:70,94:115,131:0,17:28,12:0,-34:_CDP1vx:16024,15552:67720,38:16024,15754:69134:21380,15755:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,32:5,5:900,900,73,73,62,160:68,53,61,65,63,67,65,61,71:62,73,61,160,0,0,0,0,0,0:_g1:6,8:<LR>,<LD2>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:1:1:AA,AA:175,204:95,106:0,0:9,6:_g3:721,379:214,201:,AA:_h1:((27107650&<LD2>)(27107950&<LD1>)&1&2)((27107650&<LD2>)(27107950&<LD2>)&2&1):((27107650&<LD2>)(27107950&<LD1>)&1&3&&1&3)((27107650&<LD2>)(27107671&<LD1>)&0&4)((27107650&<LD2>)(27107667&<LD1>)&1&2)((27107647&<LD1>)(27107650&<LD2>)&3&0):.:_i1:12:0,1:0,-25:.
v4  chr1    27107650    .   TAAA    T   23  Q30 ANY_VAR;SomaticQ=12;TLODQ=23;NLODQ=12;NLODV=<NONE>;TNBQF=0,-24,0,23;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,144;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-68:_A_:839:214,144:2020:721,288:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,19033:135238:9181,5335:28701:6802,4134:22812:_ADPf:248,82:608,1:187,69:495,3:_ADPr:228,97:657,1:164,70:502,0:_ALP:368,191:1148:361,166:1086:49363,22645:149301:_ARP:248,197:1108:241,180:1046:34125,25752:145120:_ALB:432,314:425,310:1804:117041,85104:492775:_ARB:439,318:400,300:1758:104098,84896:476659:_ALI:302,112:253,79:675:351,139:997:_ARI:369,162:341,144:965:476,179:1265:_AX:776,318:2207:34160,30554:133687:473,313:1866:827,318:2262:_Ax:49481,31800:91468,34918:108879,44950:651,318:696,305:_BDP:378,134:976,3:343,154:1044,1:_BT:98915,35552:257828:89851,41687:279731:3042,3794:19272:1733,4188:20088:_CDP1:121,67:412,1:93,77:427,1:121,67:412,1:93,77:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,29:9044,5319:6696,4121:0,0:0,0:878,3744:_eb:61,61:0,0:0,1:3,10:10,7:61,84:_eB:8310,5627:721,288:16,28:_eC:1436,537:47,20:40,40:821,481:33,21:36,36:_eE:801,1156:0,28:31467,20906:37,35:_eQ1:70,63:75,54:75,23:61,11:_eQ2:70,93:115,129:0,0:28,22:0,-28:_CDP1vx:16024,5874:67720,38:16024,5874:69134:21380,5875:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,19:5,5:900,900,85,115,99,160:85,63,78,76,75,76,73,80,78:99,115,74,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:4:4:AAA,AAAAA,AAAAAA,AAAA,AAA,AAAAA,AAAA,AAAAAA:61,46,15,12,80,37,33,4:39,14,9,5,47,16,13,1:0,0,0,0,0,0,0,0:2,8,2,1,2,7,5,0:_g3:721,141:214,86:,AAA:_h1:((27107650&<LD3P>)(27107950&<LD2>)&6&3&&6&3)((27107650&<LD3P>)(27107671&<LD1>)&1&7&&1&8)((27107650&<LD3P>)(27107950&<LD1>)&1&4&&2&4)((27107209&T)(27107650&<LD3P>)&3&0):((27107650&<LD3P>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:12:0,1:0,-25:.
v5  chr1    27107650    .   TAAAAA  T   6.16523 Q10 ANY_VAR;SomaticQ=-17;TLODQ=-17;NLODQ=12;NLODV=<NONE>;TNBQF=0,-33,0,1;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,144;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-68|bcDup-87:_A_:839:214,144:2020:721,288:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,19033:135238:9181,5335:28701:6802,4134:22812:_ADPf:248,82:608,1:187,69:495,3:_ADPr:228,97:657,1:164,70:502,0:_ALP:368,191:1148:361,166:1086:49363,22645:149301:_ARP:248,197:1108:241,180:1046:34125,25752:145120:_ALB:432,314:425,310:1804:117041,85104:492775:_ARB:439,318:400,300:1758:104098,84896:476659:_ALI:302,112:253,79:675:351,139:997:_ARI:369,162:341,144:965:476,179:1265:_AX:776,318:2207:34160,30554:133687:473,313:1866:827,318:2262:_Ax:49481,31800:91468,34918:108879,44950:651,318:696,305:_BDP:378,134:976,3:343,154:1044,1:_BT:98915,35552:257828:89851,41687:279731:3042,3794:19272:1733,4188:20088:_CDP1:121,67:412,1:93,77:427,1:121,67:412,1:93,77:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,29:9044,5319:6696,4121:0,0:0,0:878,3744:_eb:61,61:0,0:0,1:3,10:10,7:61,84:_eB:8310,5627:721,288:16,28:_eC:1436,537:47,20:40,40:821,481:33,21:36,36:_eE:801,596:0,18:31467,20904:37,33:_eQ1:70,58:75,48:75,1:61,0:_eQ2:70,93:115,123:0,0:28,22:0,-18:_CDP1vx:16024,3001:67720,38:16024,3466:69134:21380,3002:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,10:5,5:900,900,85,115,99,160,900,900,85,138,145,160:85,63,78,76,75,76,73,80,78,85,63,78,76,75,76,73,80,78:99,115,74,160,0,0,0,0,0,0,145,138,74,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:4:4:AAA,AAAAA,AAAAAA,AAAA,AAA,AAAAA,AAAA,AAAAAA:61,46,15,12,80,37,33,4:39,14,9,5,47,16,13,1:0,0,0,0,0,0,0,0:2,8,2,1,2,7,5,0:_g3:721,83:214,30:,AAAAA:_h1:((27107650&<LD3P>)(27107950&<LD2>)&6&3&&6&3)((27107650&<LD3P>)(27107671&<LD1>)&1&7&&1&8)((27107650&<LD3P>)(27107950&<LD1>)&1&4&&2&4)((27107209&T)(27107650&<LD3P>)&3&0):((27107650&<LD3P>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:12:0,1:0,-25:.
v6  chr1    27107650    .   TAAAA   T   6.16523 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=12;NLODV=<NONE>;TNBQF=0,-39,0,0;TNCQF=0,-1,0,0;tbDP=2020;tDP=839;tAD=214,144;t2DP=0;t2AD=0,0;RU=A;RC=18;R3X2=27107644,2,1,27107650,18,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-68|bcDup-87:_A_:839:214,144:2020:721,288:0:0,0:_Aa:2301,91,1351,100,1429,0,41,2,2176,0,7,0:41666,14477,342100,2899,121,7524,8600,90737:_Ab:484,171,5184,16203:255473,993,315291,1256:163869,162716,108,2806:_Ac:8,9:694,535,682,526:128,172,125,168:65,70,64,69:396,421,350,375:_AQ:49185,19033:135238:9181,5335:28701:6802,4134:22812:_ADPf:248,82:608,1:187,69:495,3:_ADPr:228,97:657,1:164,70:502,0:_ALP:368,191:1148:361,166:1086:49363,22645:149301:_ARP:248,197:1108:241,180:1046:34125,25752:145120:_ALB:432,314:425,310:1804:117041,85104:492775:_ARB:439,318:400,300:1758:104098,84896:476659:_ALI:302,112:253,79:675:351,139:997:_ARI:369,162:341,144:965:476,179:1265:_AX:776,318:2207:34160,30554:133687:473,313:1866:827,318:2262:_Ax:49481,31800:91468,34918:108879,44950:651,318:696,305:_BDP:378,134:976,3:343,154:1044,1:_BT:98915,35552:257828:89851,41687:279731:3042,3794:19272:1733,4188:20088:_CDP1:121,67:412,1:93,77:427,1:121,67:412,1:93,77:427,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,29:9044,5319:6696,4121:0,0:0,0:878,3744:_eb:61,61:0,0:0,1:3,10:10,7:61,84:_eB:8310,5627:721,288:16,28:_eC:1436,537:47,20:40,40:821,481:33,21:36,36:_eE:801,362:0,23:31467,20905:37,34:_eQ1:70,50:75,40:75,0:61,0:_eQ2:70,93:115,126:0,0:28,22:0,-23:_CDP1vx:16024,1802:67720,38:16024,1888:69134:21380,1803:73904:_CDP2vx:0,0:0,0:0,0:0:1,1:9:_f1:32,4:5,5:900,900,85,115,99,160,900,900,85,138,145,160,900,900,85,165,167,160:85,63,78,76,75,76,73,80,78,85,63,78,76,75,76,73,80,78,85,63,78,76,75,76,73,80,78:99,115,74,160,0,0,0,0,0,0,145,138,74,160,0,0,0,0,0,0,167,165,74,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:52,48:32,17:<LD1>,<LD2>:A,AA:_g2:4:4:AAA,AAAAA,AAAAAA,AAAA,AAA,AAAAA,AAAA,AAAAAA:61,46,15,12,80,37,33,4:39,14,9,5,47,16,13,1:0,0,0,0,0,0,0,0:2,8,2,1,2,7,5,0:_g3:721,45:214,18:,AAAA:_h1:((27107650&<LD3P>)(27107950&<LD2>)&6&3&&6&3)((27107650&<LD3P>)(27107671&<LD1>)&1&7&&1&8)((27107650&<LD3P>)(27107950&<LD1>)&1&4&&2&4)((27107209&T)(27107650&<LD3P>)&3&0):((27107650&<LD3P>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:12:0,1:0,-25:.
v7  chr1    27107667    .   AAT A   6.18389 Q10 ANY_VAR;SomaticQ=-14;TLODQ=-14;NLODQ=130;NLODV=<NONE>;TNBQF=0,-72,0,0;TNCQF=0,0,0,2;tbDP=2153;tDP=875;tAD=861,10;t2DP=0;t2AD=0,0;RU=A;RC=1;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aBQXM-32|aPositionR-56|cbDup-42:_A_:875:861,10:2153:2139,10:0:0,0:_Aa:2413,1,20,99,1428,0,65,1,2204,0,0,0:42445,14436,357480,2896,1,164,100,805:_Ab:4,1,117,339:260649,993,350808,1367:159437,170475,97,2599:_Ac:8,9:704,543,693,534:131,175,128,171:62,67,67,72:171,196,260,285:_AQ:141329,597:142166:27800,82:27917:20599,0:20599:_ADPf:625,3:631,2:487,0:487,0:_ADPr:731,7:739,1:524,0:524,0:_ALP:1088,6:1094:1044,5:1049:135262,717:136008:_ARP:1007,2:1010:970,2:973:134005,439:134566:_ALB:1605,10:1565,9:1575:426314,2151:428515:_ARB:1557,10:1467,8:1476:416463,1612:418588:_ALI:828,0:680,0:680:1011,0:1011:_ARI:1162,8:1036,8:1047:1356,10:1370:_AX:2085,10:2096:110185,76:110297:1853,10:1867:2367,10:2381:_Ax:157664,106:260557,0:337947,2443:1951,10:2096,4:_BDP:995,3:1001,2:1144,7:1152,1:_BT:262451,662:263844:308810,1746:310839:19514,92:19675:20494,207:20724:_CDP1:418,3:424,2:443,7:451,1:418,3:424,2:443,7:451,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:19,7:27120,77:20093,0:0,0:0,0:16007,7:_eb:61,61:0,0:0,2:7,12:8,7:60,68:_eB:36302,0:2139,0:17,0:_eC:11927,0:260,0:48,0:12810,0:279,0:48,0:_eE:6408,-8:0,4:134502,1364:37,36:_eQ1:69,23:91,6:91,0:60,0:_eQ2:69,77:115,125:0,2:38,13:0,-4:_CDP1vx:57218,123:57342,1:57218,215:57434:86007,124:86193:_CDP2vx:0,0:0,0:0,0:0:1,1:3:_f1:51,0:5,5:900,900,236,231,194,160:212,285,209,220,217,224,261,226,210:194,231,194,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:0,0:2,0:<LD1>,*:AT,:_g2:1:1:AT,AT:3,7:3,7:0,0:0,0:_g3:2139,10:861,10:,AT:_h1:.:((27107650&<LD2>)(27107667&<LD1>)&1&2):.:_i1:130:0,0:0,93:.
v8  chr1    27107668    .   AT  A   6.18071 Q10 ANY_VAR;SomaticQ=-14;TLODQ=-14;NLODQ=130;NLODV=<NONE>;TNBQF=0,-52,0,0;TNCQF=0,0,0,2;tbDP=2154;tDP=867;tAD=831,24;t2DP=0;t2AD=0,0;RU=T;RC=1;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aBQXM-92|aPositionR-57|cbDup-41:_A_:867:831,24:2154:2117,24:0:0,0:_Aa:2425,0,38,98,1428,0,49,3,2126,0,1,0:42039,14426,359195,2892,0,182,0,2605:_Ab:0,0,237,219:257496,986,359891,1389:153854,164637,89,2527:_Ac:8,8:702,541,698,538:130,174,129,173:62,67,67,72:175,200,259,284:_AQ:139769,1500:142046:29135,272:29512:21135,172:21307:_ADPf:613,8:626,5:471,5:476,0:_ADPr:740,12:760,8:517,0:517,0:_ALP:1083,20:1103:1049,20:1069:136101,2279:138380:_ARP:1029,6:1035:987,6:993:135873,1168:137041:_ALB:1538,23:1513,23:1536:397927,6725:404652:_ARB:1499,18:1456,18:1474:412578,4193:416771:_ALI:814,4:672,4:676:988,5:993:_ARI:1162,17:1037,15:1062:1353,20:1386:_AX:2074,25:2099:118818,1023:119937:1793,24:1830:2341,25:2379:_Ax:172116,1130:254262,1729:340628,4263:1952,25:2087,16:_BDP:971,12:988,5:1146,12:1166,8:_BT:256617,2978:260687:309418,3266:314713:18887,467:19492:20180,364:20774:_CDP1:399,12:416,5:432,12:451,7:399,12:416,5:432,12:451,7:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:21,21:28955,335:21005,171:0,0:0,0:18596,99:_eb:61,61:0,-1:0,2:7,13:10,7:60,72:_eB:37946,5:2117,8:18,25:_eC:11396,0:249,0:48,0:12558,0:274,0:48,0:_eE:6555,-5:0,7:129468,3317:37,37:_eQ1:69,32:91,23:91,0:60,0:_eQ2:69,81:115,122:0,2:38,13:0,-7:_CDP1vx:54628,527:55420,4:54628,527:55420:83010,745:84150:_CDP2vx:0,0:0,0:0,0:0:1,1:4:_f1:51,0:5,5:900,900,197,207,168,160:183,201,178,182,191,173,222,193,179:168,207,152,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:0,0:2,0:<LD1>,*:T,:_g2:2:1:TAC,T,T:6,6,12:6,6,12:0,0,0:0,0,0:_g3:2117,18:831,18:,T:_h1:.:((27107650&<LD1>)(27107668&<LD1>)&2&5&&2&5):.:_i1:130:0,0:0,93:.
v9  chr1    27107668    .   ATAC    A   6.18071 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=130;NLODV=<NONE>;TNBQF=0,-64,0,0;TNCQF=0,0,0,0;tbDP=2154;tDP=867;tAD=831,24;t2DP=0;t2AD=0,0;RU=T;RC=1;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aBQXM-92|aPositionR-57|cbDup-41|aBQXM-92|aPositionR-57|cbDup-43:_A_:867:831,24:2154:2117,24:0:0,0:_Aa:2425,0,38,98,1428,0,49,3,2126,0,1,0:42039,14426,359195,2892,0,182,0,2605:_Ab:0,0,237,219:257496,986,359891,1389:153854,164637,89,2527:_Ac:8,8:702,541,698,538:130,174,129,173:62,67,67,72:175,200,259,284:_AQ:139769,1500:142046:29135,272:29512:21135,172:21307:_ADPf:613,8:626,5:471,5:476,0:_ADPr:740,12:760,8:517,0:517,0:_ALP:1083,20:1103:1049,20:1069:136101,2279:138380:_ARP:1029,6:1035:987,6:993:135873,1168:137041:_ALB:1538,23:1513,23:1536:397927,6725:404652:_ARB:1499,18:1456,18:1474:412578,4193:416771:_ALI:814,4:672,4:676:988,5:993:_ARI:1162,17:1037,15:1062:1353,20:1386:_AX:2074,25:2099:118818,1023:119937:1793,24:1830:2341,25:2379:_Ax:172116,1130:254262,1729:340628,4263:1952,25:2087,16:_BDP:971,12:988,5:1146,12:1166,8:_BT:256617,2978:260687:309418,3266:314713:18887,467:19492:20180,364:20774:_CDP1:399,12:416,5:432,12:451,7:399,12:416,5:432,12:451,7:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:21,21:28955,335:21005,171:0,0:0,0:18596,99:_eb:61,61:0,-1:0,2:7,13:10,7:60,72:_eB:37946,5:2117,8:18,25:_eC:11396,0:249,0:48,0:12558,0:274,0:48,0:_eE:6555,-7:0,1:129468,3315:37,35:_eQ1:69,27:91,18:91,0:60,0:_eQ2:69,81:115,126:0,0:38,13:0,-1:_CDP1vx:54628,261:55420,4:54628,261:55420:83010,262:84150:_CDP2vx:0,0:0,0:0,0:0:1,1:4:_f1:51,0:5,5:900,900,197,207,168,160,900,900,197,252,216,160:183,201,178,182,191,173,222,193,179,183,201,178,182,191,173,222,193,179:168,207,152,160,0,0,0,0,0,0,216,252,152,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:0,0:2,0:<LD1>,*:T,:_g2:2:1:TAC,T,T:6,6,12:6,6,12:0,0,0:0,0,0:_g3:2117,6:831,6:,TAC:_h1:.:((27107650&<LD1>)(27107668&<LD1>)&2&5&&2&5):.:_i1:130:0,0:0,93:.
v10 chr1    27107671    .   CA  C   20  Q30 ANY_VAR;SomaticQ=20;TLODQ=20;NLODQ=114;NLODV=<NONE>;TNBQF=0,-53,0,14;TNCQF=0,0,0,20;tbDP=2235;tDP=891;tAD=868,14;t2DP=0;t2AD=0,0;RU=A;RC=9;R3X2=27107650,18,1,27107671,9,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:aPositionR-64|cbDup-53:_A_:891:868,14:2235:2208,18:0:0,0:_Aa:2484,2,27,97,1423,0,102,4,2370,0,0,0:42622,14370,368058,2886,2,118,200,2147:_Ab:8,2,294,35:258728,991,372001,1442:170323,184330,106,2695:_Ac:9,6:702,541,695,536:130,174,128,172:61,66,67,72:174,199,263,288:_AQ:145946,1140:147626:39944,238:40266:27146,182:27517:_ADPf:663,3:670,3:477,0:482,5:_ADPr:789,9:798,0:514,7:522,0:_ALP:1093,16:1116:1042,16:1064:136913,1843:139693:_ARP:1062,5:1068:994,4:999:138202,955:139308:_ALB:1632,18:1466,18:1486:389362,5980:395710:_ARB:1732,18:1706,17:1724:548017,3565:551978:_ALI:827,6:682,3:689:991,7:1004:_ARI:1256,11:1112,4:1117:1452,12:1468:_AX:2159,19:2186:204829,1138:206706:1985,18:2007:2443,19:2472:_Ax:242924,1534:254429,1507:367649,2695:1988,19:2174,19:_BDP:1019,3:1030,7:1189,15:1205,0:_BT:268434,868:271101:320641,3793:324502:19172,106:19635:20282,705:21032:_CDP1:415,3:426,7:453,11:465,0:415,3:426,7:453,11:465,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:27,23:39552,256:26885,181:0,0:0,0:33995,127:_eb:61,61:-2,-1:0,5:7,17:11,7:60,67:_eB:52875,39:2208,12:24,26:_eC:12223,0:266,0:48,0:13425,9:292,1:48,36:_eE:10705,16:0,22:135446,1916:37,37:_eQ1:69,27:92,18:92,14:60,16:_eQ2:69,76:115,125:0,20:39,14:0,-22:_CDP1vx:58822,449:59342,3:58822,449:59361:86708,682:87764:_CDP2vx:0,0:0,0:0,0:0:1,1:4:_f1:51,0:5,5:900,900,210,208,180,160:207,212,199,192,198,182,230,204,200:180,208,179,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:14,0:20,3:<LD1>,<LI1>:A,A:_g2:1:1:A,A:3,15:3,11:0,0:0,1:_g3:2208,18:868,14:,A:_h1:((27107650&<LD3P>)(27107671&<LD1>)&1&7)((27107650&<LD1>)(27107671&<LD1>)&1&3):((27107650&<LD2>)(27107671&<LD1>)&0&4)((27107650&<LD3P>)(27107671&<LD1>)&1&2):.:_i1:114:0,0:0,77:.
v11 chr1    27107950    .   G   GA  26  Q30 ANY_VAR;SomaticQ=26;TLODQ=26;NLODQ=27;NLODV=<NONE>;TNBQF=0,-40,0,26;TNCQF=0,-1,0,5;tbDP=3538;tDP=974;tAD=590,47;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1  GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-49:_A_:974:590,47:3538:2686,69:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,4620:248619:42396,1284:57940:29303,696:38757:_ADPf:934,17:1233,1:612,12:782,4:_ADPr:934,31:1240,0:676,17:890,2:_ALP:1513,35:2007:1443,34:1900:184782,4376:241910:_ARP:1642,51:2221:1586,51:2137:233494,6836:315229:_ALB:2711,76:2635,76:3542:597346,15496:801090:_ARB:2727,77:2679,76:3644:853912,24777:1178870:_ALI:970,23:895,21:1145:1288,29:1672:_ARI:1663,44:1308,24:1702:1868,48:2473:_AX:3145,77:4127:178934,5886:249376:2680,76:3604:3156,77:4145:_Ax:259035,6907:260944,5263:456654,10290:2981,77:3012,73:_BDP:1344,28:1761,2:1342,41:1777,2:_BT:358749,7511:466549:350428,9780:460981:4459,657:15370:5389,975:16545:_CDP1:299,20:493,2:291,27:481,1:299,16:493,2:291,23:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,25:41727,1284:28829,711:0,0:0,0:17895,641:_eb:61,61:1,-1:0,2:1,9:10,3:58,74:_eB:51155,557:2497,60:22,27:_eC:9058,0:205,0:48,0:9372,1:211,1:48,28:_eE:8311,161:0,17:89556,6576:37,37:_eQ1:67,48:90,38:90,26:58,0:_eQ2:67,83:115,114:0,5:39,12:0,-17:_CDP1vx:58944,1683:81457,1:63703,1810:86909:58945,1913:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,0:5,5:900,900,173,171,140,160:171,156,159,167,168,173,162,169,159:140,171,124,160,0,0,0,0,0,0:_g1:6,12:<LR>,<LI1>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:1:1:A,A:28,41:16,23:0,0:0,2:_g3:2686,69:590,39:,A:_h1:.:.:.:_i1:27:0,1:0,-10:.
v12 chr1    27107950    .   GA  G   49  Q50 ANY_VAR;SomaticQ=27;TLODQ=49;NLODQ=27;NLODV=<NONE>;TNBQF=0,-16,0,49;TNCQF=0,-1,0,22;tbDP=3538;tDP=974;tAD=590,200;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-58:_A_:974:590,200:3538:2686,436:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,30240:248619:42396,6202:57940:29303,4331:38757:_ADPf:934,138:1233,1:612,95:782,4:_ADPr:934,159:1240,0:676,112:890,2:_ALP:1513,246:2007:1443,233:1900:184782,28933:241910:_ARP:1642,285:2221:1586,270:2137:233494,40854:315229:_ALB:2711,468:2635,454:3542:597346,103293:801090:_ARB:2727,504:2679,495:3644:853912,166541:1178870:_ALI:970,155:895,140:1145:1288,207:1672:_ARI:1663,265:1308,197:1702:1868,297:2473:_AX:3145,504:4127:178934,24441:249376:2680,463:3604:3156,504:4145:_Ax:259035,34974:260944,39977:456654,67898:2981,504:3012,492:_BDP:1344,206:1761,2:1342,230:1777,2:_BT:358749,53199:466549:350428,59005:460981:4459,5292:15370:5389,5798:16545:_CDP1:299,99:493,2:291,101:481,1:299,103:493,2:291,105:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,20:41727,6028:28829,4206:0,0:0,0:17895,1188:_eb:61,61:1,-1:0,3:1,10:10,3:58,81:_eB:51155,4755:2497,436:22,20:_eC:9058,476:205,25:48,32:9372,418:211,27:48,28:_eE:8311,1298:0,32:89556,29196:37,37:_eQ1:67,68:90,59:90,49:58,59:_eQ2:67,90:115,129:0,22:39,17:0,-32:_CDP1vx:58944,11851:81457,1:63703,12013:86909:58945,12014:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,26:5,5:900,900,91,91,67,160:91,87,82,88,86,89,88,87,82:67,91,68,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:1:1:A,A:206,230:103,105:0,0:19,24:_g3:2686,436:590,208:,A:_h1:((27107859&T)(27107950&<LD1>)&8&7&&8&7)((27107950&<LD1>)(27108179&A)&8&4&&9&4)((27107650&<LD3P>)(27107950&<LD1>)&1&4)((27107949&<LD1>)(27107950&<LD1>)&3&0)((27107650&<LD2>)(27107950&<LD1>)&1&2):((27107859&T)(27107950&<LD1>)&3&3&&3&3)((27107950&<LD1>)(27108179&A)&3&1)((27107650&<LD2>)(27107950&<LD1>)&1&3)((27107949&<LD1>)(27107950&<LD1>)&3&0):((27107859&T)(27107950&<LD1>)&2&3&&2&3)((27107950&<LD1>)(27108179&A)&2&1&&2&1):_i1:27:0,1:0,-10:.
v13 chr1    27107950    .   GAA G   41  Q50 ANY_VAR;SomaticQ=27;TLODQ=41;NLODQ=27;NLODV=<NONE>;TNBQF=0,-20,0,41;TNCQF=0,-1,0,8;tbDP=3538;tDP=974;tAD=590,122;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-72:_A_:974:590,122:3538:2686,317:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,22260:248619:42396,7357:57940:29303,4107:38757:_ADPf:934,135:1233,1:612,54:782,4:_ADPr:934,103:1240,0:676,79:890,2:_ALP:1513,193:2007:1443,171:1900:184782,21637:241910:_ARP:1642,226:2221:1586,213:2137:233494,31601:315229:_ALB:2711,356:2635,348:3542:597346,77265:801090:_ARB:2727,371:2679,364:3644:853912,125175:1178870:_ALI:970,85:895,79:1145:1288,133:1672:_ARI:1663,226:1308,163:1702:1868,238:2473:_AX:3145,371:4127:178934,37093:249376:2680,348:3604:3156,371:4145:_Ax:259035,37100:260944,22165:456654,54769:2981,371:3012,366:_BDP:1344,169:1761,2:1342,148:1777,2:_BT:358749,43175:466549:350428,37692:460981:4459,4571:15370:5389,3909:16545:_CDP1:299,67:493,2:291,55:481,1:299,67:493,2:291,55:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,30:41727,7351:28829,4103:0,0:0,0:17895,4805:_eb:61,61:1,-1:0,3:1,10:10,3:58,80:_eB:51155,6188:2497,317:22,30:_eC:9058,707:205,26:48,40:9372,497:211,22:48,36:_eE:8311,1635:0,24:89556,17537:37,36:_eQ1:67,67:90,57:90,41:58,50:_eQ2:67,89:115,127:0,8:39,22:0,-24:_CDP1vx:58944,8350:81457,1:63703,8738:86909:58945,8739:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,21:5,5:900,900,105,105,90,160:102,83,89,100,99,100,98,107,89:90,105,86,160,0,0,0,0,0,0:_g1:6,8:<LR>,<LD2>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:1:1:AA,AA:169,148:67,55:0,0:21,17:_g3:2686,317:590,122:,AA:_h1:((27107859&T)(27107950&<LD2>)&7&5&&7&5)((27107650&<LD3P>)(27107950&<LD2>)&6&3)((27107950&<LD2>)(27108262&A)&5&3)((27107950&<LD2>)(27108179&A)&4&3):((27107859&T)(27107950&<LD2>)&4&2&&4&2)((27107947&<LD1>)(27107950&<LD2>)&2&2)((27107650&<LD3P>)(27107950&<LD2>)&2&2):((27107859&T)(27107950&<LD2>)&2&2&&2&2):_i1:27:0,1:0,-10:.
v14 chr1    27107950    .   GAAA    G   6.17133 Q10 ANY_VAR;SomaticQ=-20;TLODQ=-20;NLODQ=27;NLODV=<NONE>;TNBQF=0,-55,0,0;TNCQF=0,-1,0,0;tbDP=3538;tDP=974;tAD=590,10;t2DP=0;t2AD=0,0;RU=A;RC=12;R3X2=27107944,6,3,27107950,12,1 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-53:_A_:974:590,10:3538:2686,21:0:0,0:_Aa:4191,87,911,92,924,0,130,9,4095,0,8,0:45362,9521,624470,1460,110,2262,8383,70459:_Ab:449,134,2133,4358:335992,1697,596137,2462:256920,357729,96,1353:_Ac:8,7:575,446,664,513:98,132,121,162:52,57,77,82:193,218,294,319:_AQ:189279,1500:248619:42396,596:57940:29303,231:38757:_ADPf:934,8:1233,1:612,3:782,4:_ADPr:934,10:1240,0:676,4:890,2:_ALP:1513,16:2007:1443,15:1900:184782,1889:241910:_ARP:1642,13:2221:1586,13:2137:233494,1988:315229:_ALB:2711,25:2635,24:3542:597346,6693:801090:_ARB:2727,25:2679,25:3644:853912,6881:1178870:_ALI:970,6:895,5:1145:1288,7:1672:_ARI:1663,16:1308,9:1702:1868,18:2473:_AX:3145,25:4127:178934,2500:249376:2680,25:3604:3156,25:4145:_Ax:259035,2500:260944,1113:456654,3233:2981,25:3012,25:_BDP:1344,10:1761,2:1342,11:1777,2:_BT:358749,2714:466549:350428,2840:460981:4459,253:15370:5389,317:16545:_CDP1:299,4:493,2:291,6:481,1:299,4:493,2:291,6:481,1:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:22,33:41727,595:28829,230:0,0:0,0:17895,406:_eb:61,61:1,-1:0,3:1,10:10,3:58,68:_eB:51155,225:2497,21:22,33:_eC:9058,0:205,0:48,0:9372,0:211,0:48,0:_eE:8311,64:0,15:89556,1358:37,35:_eQ1:67,32:90,23:90,0:58,0:_eQ2:67,77:115,122:0,0:39,9:0,-15:_CDP1vx:58944,536:81457,1:63703,536:86909:58945,537:82306:_CDP2vx:0,0:0,0:0,0:0:1,1:7:_f1:47,0:5,5:900,900,221,226,199,160:213,199,202,215,216,207,221,215,202:199,226,187,160,0,0,0,0,0,0:_g1:6,7:<LR>,<LD3P>:49,41:22,8:<LD1>,<LD2>:A,AA:_g2:2:1:AAA,AAAA,AAA:8,2,11:4,0,6:0,0,0:0,0,1:_g3:2686,19:590,10:,AAA:_h1:.:.:.:_i1:27:0,1:0,-10:.

I would say: v2 (Q60) is likely true positive due to high QUAL. v3 v12 v13 (Q50) are undetermined in terms of true/false positive status.
v4 v10 and v11 (Q30) are likely false positive due to low QUAL. v1 v5 v6 v7 v8 v9 v14 (Q20) are very likely false positive due to very low QUAL.

some variants have Q60 some Q50 on the same location. Both are correct??

Yes, both are correct if you treat the undetermined Q50 variants as true positive. Are the sequencing data coming from a MSI-high sample? If we know a priori that the sequencing data are derived from a MSI-high sample, then the Q50 variants are more likely to be true positive. If the sequencing data come from healthy germline tissue, then the Q50 variants are more likely to be false positive. In sum, sample-specific detail can help in labeling variants as true/false positive.

Q4.

I have a truth set and saw that a lot of TRUE indels have Q50 with some of them having quality 40 (so they are borderline Q50). I guess the cut-off for tumor-only sample should be set to Q50. If I include Q40 variants, it adds 248 more INDELS. I guess most of them will be FPs.

Yes, using Q50 for InDels is good enough for tumor-only sample according to my own experience. Using Q40 is expected to add at least one false positive per 10000 genomic position, which is not acceptable in most situations.

[kokyriakidis]

Thank you for your detailed answer. From preliminary results I can say that uvc does an incredible job! I found one true variant that is detected with Mutect2 with weak evidence label. Filtering at Q50 does give me a lot less FPs than Mutect2 and Vardict!

I have some files with UMIs In the following format

A00371:69:HG73LDMXX:1:1107:17671:5572:UMI_CAGTCCAACG

I saw that uvc wants it like #CAGTCCAACG. Is there an option to specify the format of UMI in uvc?

[genetronhealth]

@kokyriakidis Thank you for your endorsement. UVC has been designed with strong theoretical foundations about NGS and human genome, and we performed tremendous amount of evaluation in-house. Even our paper (https://doi.org/10.1093/bib/bbab458) with all its supplementary materials only included a small fraction of all the evaluation that we have done.

Unfortunately, there is no option to specify the UMI format for UVC as the format can be too flexible. In the future, we might add the feature of using the auxiliary BAM tags MI and OX to denote UMI sequences, because MI and OX were specified at https://samtools.github.io/hts-specs/SAMtags.pdf and are therefore expected to be the norm in the future.

For now, you can changed the '#' into '_' in the source code at https://github.com/genetronhealth/uvc/blob/fe93440282dae784392a815e8bde0d407c7d62dd/grouping.cpp#L766 to accommodate for the format A00371:69:HG73LDMXX:1:1107:17671:5572:UMI_CAGTCCAACG

[kokyriakidis]

I was really suprised when I saw the results, especially compared to Mutect2 which is developed for so many years from NGS experts! Great work! It is extremely fast too! Waiting to see more works from you!

I change this line of code and then compile it again and it should be good?

I have seen a lot of people use the RX tag for UMIs.

[genetronhealth]

Thank you for your appreciation!

After re-compiling, it should be good as long as each read name contains exact one underscore in the input BAM.

RX is for non-error-corrected UMI, which is good enough for all practical applications. The logic should be as follows.

If MI is present, then use MI. Otherwise, if OX is present, then use OX. Otherwise, use RX.

[kokyriakidis]

Should I change both lines?

const char *umi_beg1 = strchr(qname,   '#');
const char *umi_end1 = strchr(umi_beg, '#');

[genetronhealth]

Yes. Changing both lines is better although the end result is the same from the format of " A00371:69:HG73LDMXX:1:1107:17671:5572:UMICAGTCCAACG" that you provided. Both '#' and '_' are absent from such format, so the second strchr will return a pointer to the end of qname regardless of whether the second line is changed or not.
If the "#" symbol is somehow used in the query name after the '' symbol, then definitely both lines should be changed.

[kokyriakidis]

What is your opinion for an area like this? UVC gives a pass for insertion but Q50 for deletion. Another program tells me that the deletion is artifact (which is supported in the literature by the fact that the first base of homopolymers appears in many cases to be missing). What is your opinion about this based on your experience? It is more rare to have an insertion artifact, right?

chr21   44513110    .   GT  G   45  Q50 ANY_VAR;NLODQ=15;NLODV=<NONE>;R3X2=44513102,3,1,44513110,11,1;RC=11;RU=T;SomaticQ=15;TLODQ=45;TNBQF=0,-18,0,45;TNCQF=0,-1,0,0;t2AD=0,0;t2DP=0;tAD=776,165;tDP=1211;tbDP=2238    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-84:_A_:1211:776,165:2238:1544,268:0:0,0:_Aa:2631,439,363,452,374,0,45,0,2600,0,9,0:20504,8384,391505,959,709,493,40371,34465:_Ab:2685,1118,480,670:74147,561,482511,2056:142270,247376,543,423:_Ac:8,7:444,348,649,502:66,88,117,157:44,49,85,90:179,204,246,271:_AQ:108036,18300:154236:30936,5712:47511:8354,1287:11946:_ADPf:793,125:1150,0:214,30:297,2:_ADPr:626,124:893,0:168,26:231,3:_ALP:917,171:1339:824,151:1211:93460,16015:135151:_ARP:995,196:1470:937,188:1381:145217,28027:214391:_ALB:1550,290:1476,282:2194:347821,64679:518272:_ARB:1571,296:1541,292:2278:472586,92621:696201:_ALI:281,42:238,34:342:382,56:528:_ARI:1308,232:1105,193:1602:1419,249:2043:_AX:1784,305:2551:94041,17610:152765:1534,286:2269:1801,305:2571:_Ax:136477,25508:49969,7017:326681,58614:1681,305:1740,302:_BDP:872,133:1267,0:672,135:971,2:_BT:229492,34572:334202:175191,35119:253668:2258,3160:11952:1541,3500:9015:_CDP1:419,84:665,0:357,81:546,1:419,87:665,0:357,85:546,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:21,22:30763,5623:8307,1265:0,0:0,0:6698,1000:_eb:61,61:1,-1:0,3:1,10:9,3:58,81:_eB:28458,3425:1421,268:22,22:_eC:6303,466:166,19:44,40:4573,465:122,25:44,32:_eE:12484,1832:-30,0:118075,23772:37,37:_eQ1:67,68:90,59:90,45:58,53:_eQ2:67,90:85,99:0,0:32,20:0,0:_CDP1vx:73008,14384:108772,96:73008,14522:110601:77541,14523:115101:_CDP2vx:0,0:0,0:0,0:0:1,1:8:_f1:46,25:5,5:900,900,93,92,85,160:91,80,85,88,89,86,85,89,85:85,92,83,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:67,45:0,0:<LI1>,<LD1>:T,T:_g2:1:1:T,T:133,135:87,85:0,0:8,11:_g3:1544,268:776,172:,T:_h1:((44513109&<LD1>)(44513110&<LD1>)&2&1):((44513109&<LD1>)(44513110&<LD1>)&2&1):.:_i1:15:0,1:0,-22:.

chr21   44513110    .   G   GT  67  PASS    ANY_VAR;NLODQ=15;NLODV=<NONE>;R3X2=44513102,3,1,44513110,11,1;RC=11;RU=T;SomaticQ=15;TLODQ=67;TNBQF=0,-15,0,67;TNCQF=0,-1,0,0;t2AD=0,0;t2DP=0;tAD=776,216;tDP=1211;tbDP=2238    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-87:_A_:1211:776,216:2238:1544,340:0:0,0:_Aa:2631,439,363,452,374,0,45,0,2600,0,9,0:20504,8384,391505,959,709,493,40371,34465:_Ab:2685,1118,480,670:74147,561,482511,2056:142270,247376,543,423:_Ac:8,7:444,348,649,502:66,88,117,157:44,49,85,90:179,204,246,271:_AQ:108036,21720:154236:30936,8416:47511:8354,1509:11946:_ADPf:793,180:1150,0:214,42:297,2:_ADPr:626,119:893,0:168,21:231,3:_ALP:917,200:1339:824,191:1211:93460,20093:135151:_ARP:995,222:1470:937,199:1381:145217,32432:214391:_ALB:1550,357:1476,342:2194:347821,82749:518272:_ARB:1571,356:1541,351:2278:472586,102351:696201:_ALI:281,59:238,53:342:382,63:528:_ARI:1308,280:1105,251:1602:1419,299:2043:_AX:1784,362:2551:94041,31110:152765:1534,351:2269:1801,362:2571:_Ax:136477,34009:49969,10450:326681,73022:1681,362:1740,350:_BDP:872,206:1267,0:672,134:971,2:_BT:229492,54901:334202:175191,35917:253668:2258,5198:11952:1541,3273:9015:_CDP1:419,130:665,0:357,86:546,1:419,127:665,0:357,84:546,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:21,27:30763,8414:8307,1598:0,0:0,0:6698,2960:_eb:61,61:1,-1:0,3:1,9:9,3:58,82:_eB:28458,6066:1421,312:22,28:_eC:6303,622:166,28:44,36:4573,425:122,15:44,44:_eE:12484,3317:-30,-13:118075,31383:37,37:_eQ1:67,81:90,71:90,67:58,71:_eQ2:67,91:85,86:0,0:32,23:0,0:_CDP1vx:73008,17067:108772,96:73008,18416:110601:77541,18417:115101:_CDP2vx:0,0:0,0:0,0:0:1,1:8:_f1:46,27:5,5:900,900,85,82,76,160:83,66,76,79,81,79,80,77,77:76,82,71,160,0,0,0,0,0,0:_g1:6,12:<LR>,<LI1>:67,45:0,0:<LI1>,<LD1>:T,T:_g2:1:1:T,T:206,134:127,84:0,0:16,10:_g3:1544,340:776,211:,T:_h1:((44513110&<LI1>)(44513479&<LD1>)(44513500&T)&4&0&&4&0)((44513108&<LI1>)(44513110&<LI1>)&3&1&&3&2):((44513108&<LI1>)(44513110&<LI1>)&5&1&&5&2):.:_i1:15:0,1:0,-22:.

[genetronhealth]

For homo-polymers (aka, single-nucleotide repeats), single-base deletion error rate is approximately equal to four times the single-base insertion error rate. In your case, 165 single-base deletions and 216 single-base insertions are found at this position, meaning that the single-base insertion is not an artifact and the single-base deletion is an artifact.
In sum, you are right in saying that it is more rare to have an insertion artifact.

[genetronhealth]

@kokyriakidis There does not seem to be a way to rescue it other than using some hard rescues on a case-by-case basis. (For example, use the command: bcftools view -v indels -i "QUAL>=37 && STRLEN(RU) >= 3 && RC<=3 && STRLEN(REF) < STRLEN(ALT)" #(this command get all indel variants with QUAL of at least 37 and repeat-unit length of at least 3 and repeat-count of at least 3 and of insertion type)# ) Tri-nucleotide deletion is less common than bi-nucleotide deletion in error signals.

NLODQ=105 (high) and TLODQ=20 (low) mean that the variant is highly likely to be not of germline origin and low likely to be a true biological variant.

[kokyriakidis]

One more question! Sorry for all these questions but I really enjoy the educational aspect of this conversation!

Do you think that a tri-nucleotide deletion may be FP if I detect it in a region with RC>=3? So if RC>3 is there some bigger prior that it may be FP? Or there is not difference between having RC>3 and RC<3?

[genetronhealth]

You are welcome！ The relationship between RC/RU and error rate has been investigated a long time ago by this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC149199/ which has been cited by UVC. This paper showed that STR-track length of 8 bases is the limit above which polymerase slippage happens, so we can basically classify an InDel into MSI/non-MSI types by comparing the value of RC x STRLEN(RU) with 8. In your specific example, RC<3 is different than RC>3 because STRLEN(RU)=3, so deletions with track-length = 3 x 2 and track-length = 3 x 4 belong to non-MSI and MSI types, respectively.

[genetronhealth]

In brief, RC>3 results in much bigger indel polymerase slippage error than RC<3 if STRLEN(RU) == 3.

[kokyriakidis]

So, to increase my sensitivity I guess I can include:

Q50 tri-nucleotide deletions with RC x STRLEN(RU) > 8 and Q40 tri-nucleotide deletions with RC x STRLEN(RU) <= 9 (I have a TRUE variant with Q40 RC=3 and STRLEN(RU)=3 with Q>37) and Q50 more-than-3-nucleotide deletions with RC x STRLEN(RU) > 8

[genetronhealth]

You can use the following bcftools expression: STRLEN(RU) == 3 && ((RC == 4 && QUAL>=50) || (RC == 3 && QUAL >= 40)) This expression means: repeat-unit length of exactly 3 and (number-of-repeats of at exactly 4 and QUAL of at least 50 or number-of-repeats of exactly 3 and QUAL of at least 40). The reference for bcftools expressions is at : http://samtools.github.io/bcftools/bcftools.html#expressions

[kokyriakidis]

I am really worried about the following variants that are classified as Artifacts by another programms but PASS by UVC

chr1    150849071   .   AC  A   67  PASS    ANY_VAR;NLODQ=-55;NLODV=<NONE>;R3X2=150849057,10,3,150849071,11,1;RC=11;RU=C;SomaticQ=-55;TLODQ=67;TNBQF=0,0,0,67;TNCQF=0,0,0,0;t2AD=0,0;t2DP=0;tAD=2,14;tDP=26;tbDP=74 GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:cbDup-91:_A_:26:2,14:74:6,35:0:0,0:_Aa:89,0,82,1,82,0,1,0,89,0,0,0:545,757,13247,126,0,211,0,6050:_Ab:0,0,211,426:2326,19,16237,70:6490,6846,1,125:_Ac:7,8:424,333,643,497:61,82,115,155:62,67,66,71:390,416,292,318:_AQ:420,2340:5340:152,835:2043:22,214:556:_ADPf:5,14:28,0:0,2:2,0:_ADPr:1,17:42,0:1,6:17,0:_ALP:3,22:52:3,22:52:447,2571:6469:_ARP:0,28:49:0,28:49:35,3287:6450:_ALB:0,39:0,37:80:0,10206:23849:_ARB:0,39:0,39:82:0,10068:19644:_ALI:0,7:0,5:15:1,8:19:_ARI:5,29:5,27:55:6,31:70:_AX:6,39:88:481,3135:7916:1,39:83:7,39:89:_Ax:654,3900:18,1071:2480,7965:4,39:5,39:_BDP:5,16:30,0:1,19:44,0:_BT:1486,4625:8563:117,5173:10663:69,520:819:46,842:1740:_CDP1:2,6:13,0:0,8:13,0:2,6:13,0:0,8:13,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:24,26:151,820:21,211:0,0:0,0:73,332:_eb:61,61:0,0:0,0:7,14:14,13:61,90:_eB:71,796:5,35:26,26:_eC:63,179:2,5:40,40:0,139:0,4:0,40:_eE:0,262:-30,0:319,2151:37,37:_eQ1:15,85:6,76:0,67:0,76:_eQ2:70,99:85,99:0,0:13,21:0,0:_CDP1vx:2,1128:2097,0:2,1128:2291:198,1170:2336:_CDP2vx:0,0:0,0:0,0:0:1,1:3:_f1:0,43:5,5:900,900,36,32,28,160:35,35,29,33,33,36,25,35,29:28,32,22,160,0,0,0,0,0,0:_g1:6,9:<LR>,<LD1>:67,63:0,0:<LD1>,<LD2>:C,CC:_g2:1:1:C,C:16,19:6,8:0,0:2,2:_g3:6,35:2,14:,C:_h1:((150849071&<LD1>)(150849133&A)(150849168&A)&0&4&&0&5)((150849071&<LD1>)(150849087&T)&4&0):.:.:_i1:-55:0,2:0,-92:.
chr1    150849071   .   ACC A   63  PASS    ANY_VAR;NLODQ=-55;NLODV=<NONE>;R3X2=150849057,10,3,150849071,11,1;RC=11;RU=C;SomaticQ=-55;TLODQ=63;TNBQF=0,-2,0,63;TNCQF=0,0,0,0;t2AD=0,0;t2DP=0;tAD=2,10;tDP=26;tbDP=74    GT:GQ:HQ:FT:FTS:_A_:DP:AD:bDP:bAD:c2DP:c2AD:_Aa:APDP:APXM:_Ab:APLRID:APLRI:APLRP:_Ac:ALRPxT:ALRIT:ALRIt:ALRPt:ALRBt:_AQ:aMQs:AMQs:a1BQf:A1BQf:a1BQr:A1BQr:_ADPf:aDPff:ADPff:aDPfr:ADPfr:_ADPr:aDPrf:ADPrf:aDPrr:ADPrr:_ALP:aLP1:ALP1:aLP2:ALP2:aLPL:ALPL:_ARP:aRP1:ARP1:aRP2:ARP2:aRPL:ARPL:_ALB:aLB1:aLB2:ALB2:aLBL:ALBL:_ARB:aRB1:aRB2:ARB2:aRBL:ARBL:_ALI:aLI1:aLI2:ALI2:aLIr:ALIr:_ARI:aRI1:aRI2:ARI2:aRIf:ARIf:_AX:aBQ2:ABQ2:aPF2:APF2:aP1:AP1:aP2:AP2:_Ax:aPF1:aLIT:aRIT:aP3:aNC:_BDP:bDPf:BDPf:bDPr:BDPr:_BT:bTAf:BTAf:bTAr:BTAr:bTBf:BTBf:bTBr:BTBr:_CDP1:cDP1f:CDP1f:cDP1r:CDP1r:cDP12f:CDP12f:cDP12r:CDP12r:_CDP2:cDP2f:CDP2f:cDP2r:CDP2r:_DDP:DDP1:dDP1:DDP2:dDP2:_ea:aBQ:a2BQf:a2BQr:a2XM2:a2BM2:aBQQ:_eb:bMQ:aAaMQ:bNMQ:bNMa:bNMb:bMQQ:_eB:bIAQb:bIADb:bIDQb:_eC:cIAQf:cIADf:cIDQf:cIAQr:cIADr:cIDQr:_eE:bIAQ:cIAQ:bTINQ:cTINQ:_eQ1:cPCQ1:cPLQ1:cVQ1:gVQ1:_eQ2:cPCQ2:cPLQ2:cVQ2:cMmQ:dVQinc:_CDP1vx:cDP1v:CDP1v:cDP1w:CDP1w:cDP1x:CDP1x:_CDP2vx:cDP2v:CDP2v:cDP2w:CDP2w:cDP2x:CDP2x:_f1:CONTQ:nPF:nNFA:nAFA:nBCFA:_g1:VTI:VTD:cVQ1M:cVQ2M:cVQAM:cVQSM:_g2:gapNf:gapNr:gapSeq:gapbAD1:gapcAD1:gcAD2:gcAD3:_g3:bDPa:cDP0a:gapSa:_h1:bHap:cHap:c2Hap:_i1:vHGQ:vAC:vNLODQ:note ./1:0:0,0:.:abPositionR-93|bcDup-83:_A_:26:2,10:74:6,33:0:0,0:_Aa:89,0,82,1,82,0,1,0,89,0,0,0:545,757,13247,126,0,211,0,6050:_Ab:0,0,211,426:2326,19,16237,70:6490,6846,1,125:_Ac:7,8:424,333,643,497:61,82,115,155:62,67,66,71:390,416,292,318:_AQ:420,2580:5340:152,1056:2043:22,320:556:_ADPf:5,9:28,0:0,0:2,0:_ADPr:1,24:42,0:1,10:17,0:_ALP:3,27:52:3,27:52:447,3451:6469:_ARP:0,21:49:0,21:49:35,3128:6450:_ALB:0,43:0,43:80:0,13643:23849:_ARB:0,43:0,43:82:0,9576:19644:_ALI:0,10:0,10:15:1,10:19:_ARI:5,23:5,23:55:6,33:70:_AX:6,43:88:481,4300:7916:1,43:83:7,43:89:_Ax:654,4300:18,1237:2480,5792:4,43:5,43:_BDP:5,9:30,0:1,24:44,0:_BT:1486,2452:8563:117,5373:10663:69,230:819:46,852:1740:_CDP1:2,5:13,0:0,5:13,0:2,5:13,0:0,5:13,0:_CDP2:0,0:0,0:0,0:0,0:_DDP:0,0:0,0:0,0:0,0:_ea:24,32:151,1056:21,320:0,0:0,0:73,615:_eb:61,61:0,0:0,0:7,14:14,13:61,90:_eB:71,940:5,33:26,32:_eC:63,32:2,1:40,44:0,199:0,5:0,44:_eE:0,280:-30,-8:319,1526:37,36:_eQ1:15,88:6,77:0,63:0,74:_eQ2:70,99:85,97:0,0:13,22:0,0:_CDP1vx:2,967:2097,0:2,1161:2291:198,968:2336:_CDP2vx:0,0:0,0:0,0:0:1,1:3:_f1:0,41:5,5:900,900,32,35,43,160:28,27,18,27,29,29,32,18,35:43,35,41,160,0,0,0,0,0,0:_g1:6,8:<LR>,<LD2>:67,63:0,0:<LD1>,<LD2>:C,CC:_g2:1:1:CC,CC:9,24:5,5:0,0:1,4:_g3:6,33:2,10:,CC:_h1:((150849071&<LD2>)(150849213&A)&0&7&&0&9):.:.:_i1:-55:0,2:0,-92:. 

They also have weird tAD values

But all of them have MAPQ=60 (max)

[genetronhealth]

Do you know the ground-truth for these two variants? Are they from hybrid-capture-based assays? The two variants have low depth, so the artifact signals may be caused by cross-sample contamination from another type of hybrid-capture panel.

[kokyriakidis]

Hmm I do not know the truth about them. But in other samples they are detected as NOT ARTIFACT so I guess uvc must be correct. They are from hybrid-capture-based libraries.

I did what you suggested and kept STRLEN(RU) == 3 && ((RC == 4 && QUAL>=50) || (RC == 3 && QUAL >= 40)).

I want from you one last suggestion. What about those with STRLEN(RU) > 3 and Q40 or Q50 classified as slippage from Mutect2? Should I include them or throw them away (if they exist)?

[genetronhealth]

If strlen(RU)>=4, then slippage becomes much less likely, and UVC considered this fact. Hence, for UVC, Q50 variants tend to be true positive whereas Q40 variants tend to be false negative. (similar to other types of variants).

[kokyriakidis]

Perfect!

So, STRLEN(RU) < 3 + slippage = REJECT regardless Q40 or Q50 I guess due to the higher error rate of single-double nucleotide insertio-deletion

[genetronhealth]

If I understand correctly, the most important obstacle in your evaluation is that there is a lack of truth sets? From my experience, for physical mixtures using germline variants as somatic truth sets, Q50 tend to be true positive, whereas Q40 tend to be false positive. For real high/low-TMB tumor samples, Q60/PASS tend to be true positive, respectively.
(STRLEN(RU) <3 with slippage) with high allele fraction (for example, 20% or more) is also supposed to be true positive if RC is less than 16 bps.

[genetronhealth]

Yes that works! There may be a small problem of overfitting because there are multiple filters, but I see no other obvious option to filter better anyway.

[kokyriakidis]

Q1. Should I calculate AF directly from tAD? If tAD=1899,61 I should just get the division from this metric?

Q2. Do you think I should keep uvc Q40 variants that have a PASS on Mutect2?

[genetronhealth]

1、AF is defined to be tAD[1] / (tAD[0] +tAD{1}), meaning that if tAD=1899,61 then AF (allele fraction) is 61/(1899+61). If there are more than one variant at one genomic position, then AF is better estimated to be tAD[1] / tDP, but this situation is extremely rare. Hence, tAD[1] / (tAD[0] +tAD{1}) is used. 2、Q40 variants are generally of low quality, so I recommend not keeping them unless the variant of interest is in the COSMIC database with CNT>=5. For Mutect2, what version of GATK did you use? Did you run "FilterMutect2Call"? From my experience, if you run FilterMutect2Call, then most false positive calls are removed, whereas if you did not run it, then there can still be a significant number of false positive calls.

[genetronhealth]

Hi @kokyriakidis Thank you for the evaluation. Can you describe a little bit more about your evaluation dataset and procedure? From our experience, there should rarely be any Q10 true positive variants. What does 13/17 and 12/17 mean?

[genetronhealth]

By the way, we did not evaluate UVC for calling InDels with hybrid-capture UMI-assays. I guess that might be the reason that you see a lot of false positive calls on your dataset?

[kokyriakidis]

Another question!

I am really happy with UVC results. Do you think it can be used with BAM files from RNASeq data mapped with STAR? I want to use it to detect RNA editing events (A->G, T->C, G->A, C->T) and remove likely FPs (I do not have DNASeq data to compare). Do you think a procedure like running UVC and keeping PASS,Q60,Q50,Q40 will keep most of the good candidates and remove most of the FPs?

[genetronhealth]

1 - Traditionally, AF is defined as ALT_depth / (REF_depth + ALT_depth) regardless of whether REF_depth > ALT_depth or not. Hence, it is perfectly normal that REF_depth < ALT_depth. If UVC shows REF_depth < ALT_depth but samtools/bcftools mpileup shows otherwise, please let me know. 2 - We did not evaluate with RNA-seq. UVC should remove strand-specific artifact in such a way to preserve true positive signals. I think that UVC can be used on RNA-seq data out of the box, but further evaluation is needed to ensure that UVC works well with RNA-seq data. Please note that UVC does not recognized the padded-insertion (P) cigar characters (UVC recognize the MX=IDSH cigar characters) and may simply ignore the padded insertion.