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.
Mutect2 without all normals
I have cancer samples for a set of 44 patients among which I have 11 sain controls (so, I have sain controls for 1/4 of my patients). Can I perform Mutect2 to call variants using -artefact_mode for those without controls ? Otherwise which solutions do I have to treat these patients without controls ?
Thanks for your time