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.

Mutect FA = 0 when variant Pass

Hi

I have used mutect-1.1.7, and after filtering the variants that do pass HC filters I'm looking at the frequency of the alleles. Some alleles show a frequency different from 0, but lots of them show a frequency of 0. I do not understand why this is 0 when it should be different from 0.

Example

GT:AD:BQ:DP:FA:SS 0:39,0:.:39:0.00:0

Thanks.

Tagged:

Answers

Sign In or Register to comment.