The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.