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# How did VQSR calculate the FP rate?

haopeng
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.

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.

Tagged:

## Answers

Hi @haopeng thanks so much for you question. FP rate is based on the difference between the actual Ti/Tv and the expected Ti/Tv. For more detail, see section 4 (

Tranches and the tranche plot) of this article: https://gatkforums.broadinstitute.org/gatk/discussion/11084/variant-quality-score-recalibration-vqsr