Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Hi all, I am trying to run PhaseByTransmission in a trio using the merged vcf file with father, mother and child. The vcf only contains PASS variants and no triallelic/multiallelic variants. I am also providing the ped file and it looks like that one is correct. However, during the run I encounter this error and really cannot figure out why is that? Is this because of being an indel variant? I have other indels in the file prior to this one though...
ERROR MESSAGE: Error parsing line: 1 181752783 rs798209 TG TTG 151.00 PASS 1KG_AF=.;AC1=1;AC=3;AF1=0.5;AN=6;CQ=intron_variant;DP4=102,16,89,13;DP=384;ENST=ENST00000357570;ESP_AF=.;FQ=127;GN=CACNA1E;HWE=1.000000;ICF=-1.00000;INDEL;MAF=.;MQ=48;PV4=1,1,0.11,0.14;SF=0,1,2;TYPE=ins;Cohort_AF=. GT:GQ:DP:SP:PL 0/1:99:82:0:178,0,162 0/1:99:65:3:195,0,133 0/1:99:73:3:.,.,158,
Any idea? Thanks a lot!