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.
Any filter on the .call_stats.txt output?
I'm using MuTect 1.1.4 and it works well - except I have one question about the raw output. In my project, I don't always want to filter out the variants (shown in tumor, not in normal) frequently shown in dbSNP. (it gives high value of P(germ line) in the variant classification likelihood formula.)
Does that mean I would have to use the .call_stats.txt directly please? Is there any basic filter criteria applied to this raw output? e.g. Mapping quality, base quality, allele fraction, etc. Although I don't want the algorithm deals with dbSNP and COSMIC, but I do appreciate all the other part of the MuTect design, and would like to keep them. I tried to read the original paper, but couldn't get a complete answer for this question.
Thank you in advance for your help.