Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

GATK Staff

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




Sign In or Register to comment.