Hello,
I have a family trio (parents healthy, child affected) and I am following the GATK genotype refinement workflow for detecting denovo mutations. I am particularly interested in one mutation, which I am using as a positive control (i.e. by Sanger seq I know that the child has this de novo mutation and parents are hom for the ref allele). However, when I run the CalculateGenotypePosteriors command from GATK I don't get the expected results as the father appears now to be heterozygote.
Here it is before genotype refinement:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B00_M B00_F B00_P
1 247588182 . C A 228.13 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.078;ClippingRankSum=-0.061;DP=54;ExcessHet=3.0103;FS=8.683;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.694;QD=17.55;ReadPosRankSum=-0.037;SOR=1.800;VQSLOD=4.66;culprit=MQ GT:AD:DP:GQ:PL 0/0:24,0:24:72:0,72,1024 0/0:17,0:17:51:0,51,712 0/1:5,8:13:99:259,0,175
and here it is after:
1 247588182 . C A 228.13 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-4.078;ClippingRankSum=-0.061;DP=54;ExcessHet=3.0103;FS=8.683;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.694;PG=0,0,0;QD=17.55;ReadPosRankSum=-0.037;SOR=1.800;VQSLOD=4.66;culprit=MQ GT:AD:DP:GQ:JL:JP:PL:PP 0/0:24,0:24:22:0:9:0,72,1024:0,22,974 0/1:17,0:17:9:0:9:0,51,712:9,0,661 0/1:5,8:13:99:0:9:259,0,175:209,0,235
My ped file is like this:
Family1 B00_F -9 -9 1 1 Family1 B00_M -9 -9 2 1 Family1 B00_P B00_F B00_M -9 2
Any idea why the father becomes heterozygote?
Thanks
what i believe it is because of CalculateGenotypePosteriors walker use it has updated likelihood of genotype in father please go through the entire page of this link https://www.broadinstitute.org/gatk/guide/article?id=4723