I am using GATK in a clinical context for NGS diagnosis. The issue is that the HaplotypeCaller take some time, too much time actually (2h per patient). I tried this things :
I can't use the data thread option right now, would it allow me to gain more time than the CPU option ? There is the interval option but I don't think it would allow me to gain enough time since I have gene of interest on almost all chromosomes.
I would appreciate to have your guidance regarding this problem. How would you do to make this HaplotypeCaller step faster ?
Many thanks in advance.