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 MarkDuplicates behavior
Based on what I could find on this forum, it appears that Picard's MarkDuplicate is "library-aware" (link). However, I am not exactly sure what it means. One comment in the thread says, "In our pipeline, we mark duplicates twice (once at the lane level then again after merging samples across lanes)."
Does that mean that a read-fragment which appears in two replicates run across two lanes will be marked as duplicate in the second step?