We are doing a lot of variant calling using GATK MuTect2. Evidently, multi-threading does not work in this program, so we have to run it single threaded. It takes a very long time, ~24-36 hours to finish. Anyone know how to speed it up?
I had an idea of splitting the .bam into separate files per-chromosome and then running them all separately in parrallel, but I was not sure how difficult it would be and how hard it would be to merge everything back together into a single .vcf output at the end. Any thoughts?