How is GQ calculated?

eyherabheyherabh Member
edited November 2017 in Ask the GATK team

After reading "What is a VCF and how should I interpret it?" and "CalculateGenotypePosteriors", I've been left confused about how GQ is computed. The first article seems to clearly state that GQ is computed from PL, but the second article seems to indicate that GQ is computed from GP (or PP, which I presumed it was the same). I tried to read the source code but I could only confirmed (I believe) that PP is PL plus the Dirichlet prior, but I failed to find how GQ and the genotypes are inferred after that.
I have also read previous questions related to the computation of GQ in this forum but they did not seem to me to address this problem.
Could you please clarify me whether and how GT and GQ are inferred from PL or GP/PP?
Thank you very much.

Post edited by eyherabh on

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