Notice:
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.

MuTect2 LOD calculations

Zhenyu_ZhangZhenyu_Zhang University of ChicagoMember

I am interested in how NLOD and TLOD are calculated in MuTect2. The MuTect2.java code (https://github.com/broadgsa/gatk-protected/blob/master/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2.java#L856) leads me to a function calcGenotypeLikelihoodsOfRefVsAny(), in which when a non-ref is observed:
genotypeLikelihoods[AB] += Math.log10(fpobs + (1-f)pobs/3.0d);
However, my understanding is that the real likelihood should be
genotypeLikelihoods[AB] += Math.log10(fpobs + (1-f)(1-pobs)/3.0d);

Is this an error, or could you clarify how these likelihood values, NLOD, TLOD are calculated?

I have read the algorithm guide here https://software.broadinstitute.org/gatk/guide/article?id=4442, but couldn't find my answer.
I have also read the MuTect1 paper https://www.ncbi.nlm.nih.gov/pubmed/23396013, but I don't know if they are the same as in MuTect2.

Answers

Sign In or Register to comment.