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.
I've got 300 gvcfs as a results of a Queue pipeline, that I want to combine. When I run CombineGVCFs (GATK v3.1-1) this however seems fairly slow:
INFO 15:24:22,100 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 15:57:52,778 ProgressMeter - 1:11456201 1.10e+07 33.5 m 3.0 m 0.4% 6.4 d 6.3 d INFO 15:58:52,780 ProgressMeter - 1:11805001 1.10e+07 34.5 m 3.1 m 0.4% 6.4 d 6.3 d INFO 15:59:52,781 ProgressMeter - 1:12140201 1.20e+07 35.5 m 3.0 m 0.4% 6.4 d 6.3 d
Is there a way of improving the performance of this merge? 6 days seems like a lot, but of course not unfeasible. Likewise, what kind of performance could I expect in the