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.
Recommendations for running UnifiedGenotyper on many samples
Do you have any recommendations on the settings to run many samples on UnifiedGenotyper? I'm doing 1mbp windows at this point in time with 4g memory on 3500 bam files that are about 4x depth on average.
At this point in time, jobs are estimated to last from 4 days to 5 weeks per 1mbp interval.