I am trying to incorporate genotype likelihoods into a downstream analysis. I have two questions:
1) Why is the most likely genotype scaled to a Phred score of zero?
2) Is there a way to undo the scaling? I have seen downstream tools undo the scaling, but I don't know how they do it. Is there an equation that will return an estimated genotype likelihood from the scaled genotype likelihoods?
Thank you for your time.