We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Questions about calculating the genotype likelihoods
In this website, https://software.broadinstitute.org/gatk/documentation/article.php?id=4442, you showed the formula used to calculate PL.
I can understand most of the formulas used here. But I can't understand the change on the formula when you are trying to implement G=H1H2 to P(D|G). I tried a lot of times and I cannot finish the math inference on my own. I think the formula you used to calculate P(D|G) should also be available to be generated by pure math deduction.
Therefore, if convenient, would you please show me the process of the math deduction of the formula to prove that P(D|G)=P(D|H1)/2 + P(D|H2)/2 (given a single read sequence).