Heads up:
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.

Mutect1 multi-allelic cases

ersenkavakersenkavak TurkeyMember
edited March 4 in MuTect v1

We have worked hard to figure this out.
By default, or by using any parameters, Mutect1 does not catch multi-allelic cases at a single position. It seems to pick one of the alternate alleles at every position (randomly?). As in mutect2, one expects ploidy like parameter. We need to detect every alternate allele at that position, as somatic analysis requires this.

Do you have an idea? How should one use Mutect1 for detecting multiallelic cases?


Post edited by ersenkavak on
Sign In or Register to comment.