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.
Tool in GATK to gather BQSR reports
I would like to request a feature from the GATK developers to be included in the toolkit. To parallelize BQSR, it is necessary to merge the GATK BQSR reports. I found the following post from a few years ago stating that the tool to gather BQSR reports would be out shortly: http://gatkforums.broadinstitute.org/gatk/discussion/1919/parallelizing-base-quality-score-recalibration
Could you please add this tool to GATK? Not all folks use Queue, and it seems like this is generally useful when trying to parallelize BQSR on large datasets to make it complete in a reasonable amount of time. Given the main method is only a few lines of code, a GATK developer should be able to get this done very quickly.