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:
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?