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.
HaplotypeCaller on sliced BAMs
I'm trying to do germline calling using HaplotypeCaller. However, I'm only interested in obtaining germline variants for a subset of the genome. To save space and compute resources, I was hoping to use a sliced BAM that includes reads spanning only my regions of interest. Can HaplotypeCaller handle such sliced BAM files and correctly infer germline SNPs for those regions ?