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.
Indel Realigner using SNPs
I was just wondering, would it not be benefitial to use a database of SNPs togheter with the indels database during the indel Realigner step? I can be wrong, but it makes sense to me that knowing the location of the SNPs would facilitate the indel realignment step...