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.
Reversions: an Algorithm issue
Since this is an algorithm question that covers both types of MuTect, I'd rather raise it here.
I have noticed the variant calling model in MuTect seems to require AF[TUMOR] > AF[NORMAL] to be called. This implies that a reversion/ back mutation, i.e. AF[TUMOR] < AF[NORMAL], will not be called. Is there any rationale to this?