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 you use Mutect2 with non-human samples?
I want to use Mutect2 to subtract out variants present in a wild-type sample from variants present in an organism displaying a desired phenotype. Is Mutect2 appropriate for this? Can I use my wild-type .bam as the normal and the mutant phenotype .bam as the tumor? Do I need to create a PoN for this case? I only have two wild-type .bams