MuTect2 LOD calculations

Zhenyu_ZhangZhenyu_Zhang University of ChicagoMember

I am interested in how NLOD and TLOD are calculated in MuTect2. The code ( leads me to a function calcGenotypeLikelihoodsOfRefVsAny(), in which when a non-ref is observed:
genotypeLikelihoods[AB] += Math.log10(fpobs + (1-f)pobs/3.0d);
However, my understanding is that the real likelihood should be
genotypeLikelihoods[AB] += Math.log10(fpobs + (1-f)(1-pobs)/3.0d);

Is this an error, or could you clarify how these likelihood values, NLOD, TLOD are calculated?

I have read the algorithm guide here, but couldn't find my answer.
I have also read the MuTect1 paper, but I don't know if they are the same as in MuTect2.


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