How to parallelise HaplotypeCaller in 4.0.0?
At this time, what is the recommended way to parallelise HaplotypeCaller in GATK4, please? Assuming I care about results and don't want to use the Spark version. In particular, what is the effect of nativePairHmmThreads? So far it has had no influence on the speed of my runs, and yet runs with the same parameters can vary drastically in length (with the record ones taking over a month on a vey diverse insect...).