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.
Reassign all mapping qualities above a certain value
I'm trying to do variant calling on RNA-seq data aligned with Tophat. I know that I need to use SplitNCigarReads, but I'm having some trouble reassigning mapping qualities. I can successfully reassign MQ of 255 as suggested in the best practices, but am still getting errors for MQ values that are above 60. Is there any way that I can reassign all mapping qualities above a certain value? It seems like there's only tools to do this for one specific MQ and not an entire range.