Question: How do I interpret genotype likelihood in the VCF format?
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gravatar for colin.kern
5 months ago by
colin.kern290
United States
colin.kern290 wrote:

I've run FreeBayes on a few samples, but I'm not sure how to interpret the GL (genotype likelihood) part of the VCF format. As an example, here is the info from one of the samples:

GT:DP:AD:RO:QR:AO:QA:GL 0/1:28:13,15:13:521:15:611:-46.8976,0,-38.8067

I understand that there are 13 reads with the reference allele and 15 reads with the alternate allele, but I don't understand exactly what the p-values represented in the GL part are the significance values for, and why there are three values. The description I've found for GL is "Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy.". So is it the p-values of 0/0, 1/1, and 0/1? What is the order? And why is one of them always log10 p-value of 0?

snp vcf • 290 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by colin.kern290
2
gravatar for colin.kern
5 months ago by
colin.kern290
United States
colin.kern290 wrote:

Ok, it seems like the order is 0/0, 0/1, 1/1, but the numbers are normalized by the most likely genotype, which will therefore always be 0.

ADD COMMENTlink written 5 months ago by colin.kern290
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