how to understand this "1/1:0,1:1:3:36,3,0" in VCF?

rcholicrcholic DenverPosts: 68Member

One of my samples has this entry "1/1:0,1:1:3:36,3,0" in the information field, and from my understanding, the genotype is homo variant, because it has 1/1. However, I do not understand why. Since it has 0 REF reads and has only 1 ALT read, how does GATK tell this variant is a homo variant??


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,428Administrator, GATK Dev admin

    This is GATK's best guess based on the data -- well else could it say considering there is some evidence for ALT, but none for REF? But obviously genotype confidence will be extremely poor since the data is so scarce.

    Geraldine Van der Auwera, PhD

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