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.
MuTect v2 t_LOD filtering
we actually use GATK3.5 in combination with MuTect v2 to identify somatic variants. In the output, both FoxoG and t_LOD scores are listed. However, I see a predominance of C>A mutations (appr. 70%) and wonder, whether the variants are already filtered for oxidation induced changes as described by Costello et al. (PMID 23303777). If I do calculations for the C>A variants I get approximately half t_LOD values above the threshold (-10+(100/3)*FoxoG) - i.e. the "good ones" - and another half below (the putative artifacts). So, I suppose that filtering has not been done - is that right?
Thanks for your help - Stefan