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.
Picard metrics definitions
I was taking a look at the documentation about the duplication metrics of MarkDuplicates and I have some doubts. Is the UNPAIRED_READS_EXAMINED field taking into account only primary alignments or also secondary and supplementary alignments?