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UVC, a very accurate small-variant caller (https://doi.org/10.1093/bib/bbab458)

License: BSD 3-Clause "New" or "Revised" License

C++ 96.68% Makefile 0.48% C 0.94% Shell 1.57% Python 0.34%

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cmguodong zhaoxiaofei schaudge yunqing19

uvc's Issues

Parameters or preprocessing steps to improve uvc performance

Hello,

I used mutect2, vardict, and varscan to call variants on matched tumour-normal bam files containing reads that were UMI-collapsed with fgbio's CallDuplexConsensusReads and stitched using illumina's pisces/gemini. I used UVC on reads that had UMIs extracted and placed in the reads QNAME before being realigned to hg19 (but with no UMI collapsing or read stitching).

The variants called by Mutect2 (with FilterMutectCalls applied) align well with the gold standard list of variants for this matched tumour-normal pair. The variants predicted by varscan with basic filters applied (VAF > 0.05, somatic_status=Somatic) also align well with this goldstandard list of variants. Vardict labels many passing variants, but also captures many of the gold standard variants.

UVC is capturing 3 less variants than mutect2/vardict and 5 less variants than varscan. I am wondering if I should change any parameters when running uvc or perform additional steps in the preprocessing of my tumour-normal bam files. Below is an outline of my current workflow:

Current preprocessing steps:

picard FastqToSam
fgbio ExtractUMIsFromBam (get reads in originalName#UMI format)
picard SamToFastq
bwa (for alignment)

Current uvc script:
uvc='/software/uvc/0.14.2.15f4adc/bin/uvcTN.sh'
export UVC_BIN_EXE_FULL_NAME=/software/uvc/0.14.2.15f4adc/bin/uvc-1

$uvc ${REF_GENOME} ${TUMOUR_BAM} ${NORMAL_BAM} \
${OUTPUT_PATH}/colo829_uvc.vcf "COLO829_S8,COLO829_BL_S7"

Apologies for the long description, thank you for your advice.

how to understand these different values between SRR7757440_SRR7757439_TN.vcf.gz and SRR7757440_uvc1.vcf.gz

Hi Zhao,

I have some questions about the result.

how to understand these different values between SRR7757440_SRR7757439_TN.vcf.gz [a] and SRR7757440_uvc1.vcf.gz [b], just like 'QUAL', 'FILTER', especially 'SomaticQ'
[a] 3 16306504 . C T 60 PASS SOMATIC;SomaticQ=60;TLODQ=78;NLODQ=60;NLODV=A;TNBQF=251,26,0,19;TNCQF=177,48,0,62;tDP=50250;tADR=50127,78;nDP=58463;nADR=58416,6;
[b] 3 16306504 . C T 49 Q50 ANY_VAR;SomaticQ=49;TLODQ=49;NLODQ=57;NLODV=;TNBQF=0,-75,0,4;TNCQF=0,-75,0,49;tDP=50250;tADR=50127,78;nDP=0;nADR=0,0;

(##INFO=<ID=SomaticQ,Number=A,Type=Float,Description="Somatic quality of the variant, the PHRED-scale probability that this variant is not somatic.)
SomaticQ value of [a] means this variant is not somatic and has a high PHRED-scale probability (60，1 - 10e-6), but the value of allele ([a] tADR=50127,78 ) shows that this variant may be a low freq mutation.
am I misunderstanding these?

thanks

uvc1 was not found in /uvc-master/bin/

as describe above, uvc1 was not found in /uvc-master/bin/

UVC results

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:.

Preprocessing BAMS to get originalName#UMI format

Hello,

To get my reads into the originalName#UMI format in a bam file, I am running:

picard FastqToSam
fgbio ExtractUMIsFromBam (get reads in originalName#UMI format)
picard SamToFastq
bwa (for alignment)
However, when using fgbio ExtractUMIsFromBam with --annotate-read-names set to true, the UMI tag is appended to the QNAME but with a + instead of a #. Although I can reformat the bams, I was wondering if there were any alternative pre-processing steps or tools that should be used prior to running UVC?

Tumor only variant calling

Hi!

Do you have any recent benchmarks regarding Tummor only variant calling? I was about to try Mutect and PureCN when I saw your implementation.

Thanks,
Konstantinos

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