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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.