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.
VQSR on SNP and Indel
My impression is that old recommendation from the GATK team is to do VQSR on
indel.vcf separately and in parallel. But the current pipeline and example is to do them sequentially on
I wonder if the new approach is to keep those variants that are neither SNP nor Indel?