The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Why is BaseRecalibrator so slow - not using all threads?
I'm running BaseRecalibrator on a full lane of HiSeq. I set the -nct switch to 8, but I see that the average load is <1. Why is this so? Doesn't the BaseRecalibrator use threads properly?
I've seen this thread http://gatkforums.broadinstitute.org/discussion/1263/baserecalibrator-trade-off-between-runtime-and-accuracy on how to speed up the process by downsampling. Is this a better option considering I have >200M reads?
BTW I'm using version 2.2-8 - do newer versions implement -num_threads?
I would really love to reduce the runtime from 36hrs.