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.
Using intervals in Mutect2
I would like to spread a Mutect2 run out over several intervals in order to speed it up. I am using the GATK hg38 resource bundle reference. Do I need to put in a separate interval for each contig or will listing "chr2" (for example) also include all the alternate contigs that map to chromosome 2?