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Old 08-20-2012, 06:40 AM   #1
Karen Chait Berman
Junior Member
Location: Israel

Join Date: May 2012
Posts: 4
Default Incorrect Genotype information in VCF


I am working with samtools and I get variants with genotypes that do not make sense. The DP4 shows high number of reads that match the reference G (101) and only 25 reads that match the Alt A (16,9) but the genotype is homozygote AA acording to the PL.

SL2.40ch05 14606139 . G A 151 . DP=129;VDB=0.0365;AF1=1;AC1=2;DP4=101,0,16,9;MQ=30;FQ=-28;PV4=1.2e-07,1,1,1 GT:PL:GQ 1/1:180,1,0:4

another example:
SL2.40ch05 14606550 . T A 125 . DP=186;VDB=0.0399;AF1=1;AC1=2;DP4=1,146,15,22;MQ=29;FQ=-53;PV4=3.3e-11,1,1,1 GT:PL:GQ 1/1:158,26,0:49

does anybody know how do get the correct genotype?
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