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

rcholicrcholic DenverMember

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??

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie 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.

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