SEQanswers genotype likelihoods calculation of GATK
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 04-03-2012, 06:35 AM #1 lyz1030 Member   Location: USA Join Date: Mar 2011 Posts: 33 genotype likelihoods calculation of GATK Hi all, I have a question about the genotype likelihoods calculation of GATK (see the source code annotation org.broadinstitute.sting.gatk.walkers.DiploidSNPGenotypeLikelihoods.java) For heterozygous genotypes and if bi is in G, I do not konw why P(bi | G) = 1 - P(error | q1) / 2 + P(error | q1) / 6, I think P(bi | G)=1/2 (1- P(error | q1) + P(error | q1)/3)=1/2 -P(error | q1)/3. Take G=AC for example, P(bi | AC)=1/2(P(bi | A)+P(bi | C)). If bi=A, then P(bi | G)=1/2 (1- P(error | q1) + P(error | q1)/3). Could anyone explain it for me?