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.
Can Mutect2 be applied in tumor only mode for somatic variant detection?
I see in your documentation for Mutect2 you state: "MuTect2 currently only supports the calling of a single tumor-normal pair at a time"
However, it appears to work in tumor only mode as well, at least for the creation of the panel of normals.
My question is can Mutect2 be applied in tumor only mode (simply with no normal provided and not using the artifact_detection_mode flag) to detect accurate somatic variants when a normal sample is not available (similarly to what could be done in mutect1)?