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.
Somatic mutations based on sliced bam
I would like to retrieve simple somatic mutations (using mutect2) from a bam file. However, I am interested in mutations in specific areas in the DNA only (for example, specific chromosoms). Can I calculate the mutations based on a sliced bam file? or should I first run the tool to generate the somatic mutations file, and then slice it?