no. of cores utilization in haplotypcaller in GVCF mode
I am running Haplotypecaller (v220.127.116.11) (not the spark version) on some WGS samples on a SGE (Sun grid Engine) cluster. When I am submitting a job to my cluster, I am asking for 1 core (on an 8 core processor having 1 thread each). I am aware that in native haplotypecaller, I cannot mention the number of cores it should utilize for parallelization and only use --native-pair-hmm-threads to make that step faster (whose default is 4).
Does Haplotypecaller utilize cores according to the availability? I mean if I am assigning 1 core to that job, will it still try to utilize other cores on that processor?
Kindly let me know if you need any more information for clarity.