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.
GATK best practices for exome/targeted capture (small region)
I was wondering if there is a set of best practices developed specifically for calling variants from a small region target capture sample. I looked but I could not find a one-stop comprehensive documentation. If not, are there some specific recommendations (such as certain values of parameters for the exome/targetome analysis? For eg., -L.