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.
We have a problem with GATK DepthOfCoverage, it is running too slow. With default parameters, it took 12 hours on Amazon c4.2xlarge instance for a BAM of 125MB. We are running at this moment another task on c4.8xlarge, with -nt parameter set to 36 and --OmitIntervalStatistics, but it seems multithreading does not work. Can someone help with this? Or maybe suggest some other tool with similar funcionality?