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.
grch37-lite in Call Somatic Mutations WGS
TARGET WGS data was aligned to GRCH37-lite. Internally, GP has aligned to Hg19. Is there a easy way to merge the two together without having to realign the TARGET data (and take up a lot of space realigning)?
I ask since I'm trying to use Call Somatic Mutations WGS in firehose but because GRCH37-lite is slightly simplified, there are contigs that are missing and thus the process fails.
Alternatively, are there annotations somewhere for the GRCH37-lite that I could use? I don't see it on Algorithms Commons.
(Sorry if this is an over simplification... I'm still pretty new to this)