To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Seems Not The Right Genotype of My variants

Hello this is my GT:AD:DP:GQ:PL information of my variants : 0/1:4,42:46:11:1429,0,11 . It seems that "1/1" might the best genotype of my variant, can anybody tell me the reason.
This is my command: genotyping_mode DISCOVERY --emitRefConfidence GVCF -stand_call_conf 10



  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    edited March 9


    If you look at the PLs, you see the tool is not super confident whether the genotype is het or hom var. In this case, there was a bit more confidence in the het call, probably due to high base qualities for the ref allele. If you can use the Genotype Refinement Workflow, that may help with cases like this.


    P.S. Have a look in the Methods and Algorithms section for an explanation of how genotypes are called.

Sign In or Register to comment.