Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!
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.