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.
Use all samples or group samples for GenotypeGVCFs?
I have created g.vcfs for all my samples (48). Half of my samples (24) are control individuals and the other half (24) is treated individuals. Should I run
GenotypeGVCFs on all my samples once to generate one raw vcf? Or twice, once for treated samples and once for control samples producing two raw vcfs? Ultimately I am looking for differences between my groups.