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.
BWA mem -M option
bwa mem has an -M flag that will:
Mark shorter split hits as secondary (for Picard compatibility).
However, my guess is Picard has since been updated and this is no longer required. Should bwa mem be run with or without the -M flag assuming we are using relatively up to date software?