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.

In which step exactly the allele depth / frequency is used during variant calling?

UniCornUniCorn USMember
edited April 2018 in Ask the GATK team

I was thinking of how allele depth / frequency affect variant calling. I know that the HC is using Bayes to call variant. The question is how is allele depth / frequency information used during the variant calling?

Based on Bayes: The most possible variant allele is: P(G|D) = arg max P(G) * P(D|G). I initial thought that P(D|G) is the allele frequency of data. But feel something is not right.

Could you please share some comment? Thanks

Best Answer

Answers

Sign In or Register to comment.