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.
Advice for running GenotypeVCF and Recalibration on a thousand samples
I am working with a couple thousand gVCFs. I plan to run GenotypeGVCF and ApplyRecalibration on them in a joint fashion. I want to know how does GATK scale on these numbers, and is it even recommended to run this analysis on these numbers?
I tried running GenotypeGVCF in multi-threaded mode, but it runs into race condition (or some other issue) and a single thread seems the only viable option.