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How did VQSR calculate the FP rate?

haopenghaopeng ChineseMember
Dear GATK development colleagues,

I have a small question regarding how to calculate TP/FP in the tranch plot.
I understand we calculate the TP rate based on the "truth" set (i.e.
of the SNPs in the truth set, how many are called. ).

My question is: how did VQSR calculate the FP rate?
I read the VQSR manual, cannot find the answer to this question.
would appreciate your help here for this question.


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