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HaplotypeCaller variant with 0/0 genotype

zuoxyzuoxy ChinaMember

There are some confused result found in the output gvcf of HaplotypeCaller. Why the genotypes is 0/0 but called a GC->G deletion? see below for example.

chr8 118915071 . GC G,<NON_REF> 0 . DP=37;MLEAC=0,0;MLEAF=0.00,0.00;MQ=60.29;MQ0=0 GT:AD:DP:GQ:PL:SB 0/0:35,0,0:35:99:0,104,1078,105,1079,1080:27,8,0,0
chr8 118915072 rs34953549 CA C,<NON_REF> 0 . BaseQRankSum=1.783;ClippingRankSum=-0.149;DB;DP=40;MLEAC=0,0;MLEAF=0.00,0.00;MQ=60.27;MQ0=0;MQRankSum=0.743;ReadPosRankSum=1.296 GT:AD:DP:GQ:PL:SB 0/0:25,3,0:28:24:0,24,331,71,340,387:18,7,0,0

Thanks a lot!



  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Hiu,

    Can you please confirm that you are using the latest version of GATK (3.3)? Please also post the exact command you used to get this result. Also, can you post the IGV screenshot of the bamout file for this region?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @zuoxy Keep in mind that this is a gvcf, which contains intermediate information, not final variant calls. What you see here means that HaplotypeCaller saw something that looked like it could be a GC->G deletion, but found that the evidence was inconclusive (note the presence of two PL values = 0). The caller recorded this information in the gvcf because it could be relevant when running joint genotyping. That does not mean it is calling the variant as such.

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