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How does unified genotyper calculate prior probabilities for one sample?

Hello,

I was reading the documentation found on this webpage
http://gatkforums.broadinstitute.org/gatk/discussion/1237/how-unified-genotyper-works-retired#latest

It says that the priors are calculated during multi-sample calculation. I, however, just has the sequence data from one sample with 80X depth coverage (I'm not sure if that's relevant but my understanding is that it does allow for calling of high confidence variants). So I was wondering how the priors would be calculated in this case. Thank you!

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    In that case it's calculated with a somewhat simpler model which is explained in the recent workshop presentations for HaplotypeCaller. The genotyping part (step 4 of HC) is the same in UG.

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