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.