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.
Effect of Queue scatter+gather on HaplotypeCaller?
I have a question about choosing the number of scatter jobs when running the HaplotypeCaller in Queue.
Basically, is there a hard and fast rule about how small you can split up the job? From what I understand of HC, given it does local reconstruction of haplotypes anyway, splitting into more jobs shouldn't affect the results.
(My current dataset is mouse whole-genome data with 24 samples, and even scattered into 250 jobs, the longest jobs still took ~6d to run... I'd love to be able to speed it up if I have to re-run HC by splitting into more jobs. As long as it doesn't affect the results!)