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DP in multiple sample SNP calling didn't match when viewed in alignment file

crop_bioinfocrop_bioinfo knoxvilleMember
edited August 2016 in Ask the GATK team

I did call SNP with three samples together and here is a line of vcf file:
scaffold_1 67412 . A G 4591.64 PASS AC=3;AF=1.00;AN=3;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.15;SOR=0.731 GT:AD:DP:GQ:PL 1:0,83:83:99:3785,0 1:0,12:12:99:404,0 1:0,11:11:99:430,0

DPs are not maching at locus 67412: Figure 2 has 10 reads in a particular locus but DP is 12 in vcf and Figure 3 has 9 but DP is 11

Multiple SNPs called together: Figure1: 1:0,83:83:99:3785,0 Figure2: 1:0,12:12:99:404,0 Figure3: 1:0,11:11:99:430,0

image

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