Number of cores vs core speed

I know you do not give hardware recommendations but can you tell me what is more important for GATK 4? More cores or the speed of a single core? In GATK 3 you could use -nct for parallelization, but this does not seem to exist in GATK4 anymore.



  • After some reading it seems parallelization will be added back in with SPARK, even on single machines. If I want to take advange of parallelization I should stick to GATK3 for now until SPARK Tools are out of beta. Did I get this right?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    You are free to try out the Spark tools, but some are still in beta. In general, all GATK4 tools are faster than GATK3 tools, so it may be worth it to simply upgrade to GATK4.


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