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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
re-scaling genotype likelihoods
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.