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.
Details on how Picard-Tools define duplicate reads
I am trying to implement a script to group duplicate reads into families and would like to understand which criteria Picard's MarkDuplicates uses. I've read that it compares the 5' ends of reads (either single-end or paired-end), but haven't found much more. Is there any page or publication where these details are provided?