GATK4 BaseRecalibrator multithreading (not Spark)
I'm using GATK4 in a VM with 16 Intel Xeon E7-4860 processors (they can't support AVX), and 32 Gb RAM + 16 Gb swap (I can ask more).
Since GATK4 doesn't have the multithreading options (-nt and -nct) anymore, I oftenly cannot take advantage of all processors. Because of this, I have been trying the Spark version of the tools, but I don't really want to use them until you "aprove" them oficially.
For other tools I have been using a workaround dividing the genome in intervals and run the tools using the -L option on 16 parallel commands; and then merging the results. But BaseRecalibrator can't be applied like this.
Is there any option that I'm missing to be able to run BaseRecalibrator more efficiently?