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.
CollectHSMetrics - how to create Bait and Target intervals?
I've been banging my head on this one for quite some time and after countless searching, nothing really has answered my question. I downloaded some BAM files off of TCGA. After running the MarkDuplicates and BamIndex through Picardtools without any error, I wanted to run the CollectHsMetrics tool, but I keep getting the error "Interval list file must contain header". I'm temporarily using an interval list grabbed from somewhere else (which I'm sure it won't work) just to see if I can get the CollectMetrics to work.
I guess my main question is HOW do I obtain or create Bait and Target intervals from sample BAM files downloaded from the TCGA? From previous searches people have run BedTools on Bed files but I did not receive any of those when the raw BAM files were downloaded. Thank you kindly for you help and patience - I'm super new at this so my apologies.