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UnifiedGenotyper EMIT_ALL_SITES and probabilities at monomorphic sites

tommycarstensentommycarstensen United KingdomMember ✭✭✭
edited May 2013 in Ask the GATK team

I have used UnifiedGenotyper with the EMIT_ALL_SITES option on selected sites of interest. However, in some cases a genotype is called (see below), but no probability is given. Is it possible to force UG to write those probabilities?

Here is a monomorphic site for which no probabilities are given:
1 100008719 . C .13.19 . AN=76;DP=70;MQ=55.57;MQ0=0 GT:DP ./. ./. 0/0:2 ./. 0/0:1 0/0:2 0/0:2 0/0:1 ./. 0/0:2 0/0:3 0/0:2 ./. 0/0:1 0/0:1 0/0:3 ./. 0/0:2 ./. ./. ./. 0/0:1 0/0:1 0/0:3 0/0:1 ./. 0/0:1 0/0:1 ./. 0/0:1 0/0:1 ./. 0/0:2 ./. ./. ./. 0/0:3 ./. 0/0:1 0/0:1 0/0:2 ./. ./. ./. 0/0:2 ./. 0/0:1 ./.0/0:1 ./. ./. 0/0:3 ./. 0/0:1 0/0:3 0/0:1 0/0:2 ./. 0/0:1 0/0:3 0/0:3 ./. 0/0:2 ./. ./. 0/0:1 ./.

Thank you.

I think I can solve my problem by using the GENOTYPE_GIVEN_ALLELES option in UG. I'm currently checking it.

Post edited by tommycarstensen on

Best Answer

Answers

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭
    edited May 2013

    GENOTYPE_GIVEN_ALLELES did indeed sort my problem. Here is the output after using it:

    1 100008719 . C T 33.63 . AC=7;AF=0.060;AN=116;BaseQRankSum=-5.506;DP=131;Dels=0.00;FS=21.362;HaplotypeScore=0.9374;InbreedingCoeff=-0.1132;MLEAC=8;MLEAF=0.069;MQ=54.05;MQ0=0;MQRankSum=-3.887;QD=2.24;ReadPosRankSum=0.184 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6:0,6,74 0/0:2,0:2:6:0,6,77 ./. 0/0:1,0:1:3:0,3,33 0/1:1,1:2:19:19,0,20 ./. ./. ./. ./. 0/0:3,1:4:6:0,6,79 ./. ./. 0/0:1,0:1:3:0,3,39 0/1:2,1:3:23:23,0,64 ./. 0/0:5,0:5:15:0,15,185 0/0:1,0:1:3:0,3,39 0/0:2,1:3:6:0,6,79 0/0:2,0:2:6:0,6,71 ./. ./. 0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,69 0/0:2,0:2:6:0,6,79 0/0:1,0:1:3:0,3,39 ./. 0/0:1,0:1:3:0,3,40 ./. 0/0:2,0:2:6:0,6,78 0/0:3,2:5:6:0,6,60 ./. ./. ./. 0/0:3,0:3:9:0,9,114 ./. 0/0:1,0:1:3:0,3,39 0/1:2,1:3:20:20,0,60 0/0:3,0:3:9:0,9,98 ./.0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,77 ./. ./. 0/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 0/0:2,0:2:6:0,6,79 0/0:1,0:1:3:0,3,33 ./. ./. 0/0:4,0:4:12:0,12,142 ./. ./. 1/1:0,2:3:3:23,3,0 0/0:1,0:1:3:0,3,27 0/0:1,0:1:3:0,3,33 ./. 0/0:1,0:1:3:0,3,32 0/0:1,0:1:3:0,3,22 ./. ./. 0/0:2,1:3:6:0,6,68 0/0:2,0:2:6:0,6,59 ./. ./. 0/0:4,0:5:12:0,12,156 ./.0/0:2,1:3:3:0,3,38 ./. ./. 0/0:1,0:1:3:0,3,38 0/0:1,0:1:3:0,3,38 ./. 0/0:3,1:4:9:0,9,118 ./. ./. 0/0:2,0:2:6:0,6,79 0/1:1,1:2:20:20,0,33 0/1:1,1:2:17:17,0,32 0/0:2,0:2:6:0,6,76 0/0:3,0:3:9:0,9,118 0/0:1,0:1:3:0,3,25 0/0:1,0:1:3:0,3,360/0:2,0:2:6:0,6,72 ./. 0/0:2,0:2:6:0,6,77 ./. ./. 0/0:1,0:1:3:0,3,30 0/0:3,0:3:9:0,9,117 0/0:1,1:2:3:0,3,39 0/0:2,0:2:6:0,6,59 ./. 0/0:1,0:1:3:0,3,37 0/0:1,0:1:3:0,3,38 ./. 0/0:5,0:5:12:0,12,154 ./. ./. 0/0:2,0:2:6:0,6,73

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