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.
KnownSites for non-human data - generate them with UG or HC?
I am working on non-human data and want to use GATK's Haplotype caller to call variants. I am using the protocol that your team recommends.
So far I have reached the indel realignment stage and want to do base recalibration next. Since I do not have known sites, elsewhere in the forum you advise doing initial round of SNP calling on original un-recalibrated data.
Should I do Is this initial calling with UnifiedGenotyper on the indel realigned BAMs, or since I want to use Haploytype Caller downstream, should I use this walker instead?
Thanks for your input!