Is --native-pair-hmm-threads in GATK 188.8.131.52 same as -nct in older GATK versions?
I did not find anything to assign number of threads to be used for the job (ex haplotypecaller)..I beleive it was removed or named something else..did not specifically find anything in haplotycaller help options..
You have to use Spark versions of the tools available to use multithreaded acceleration. Other than that there is no multi threading option available. Spark versions of the tools can be run locally without the need of a cluster.
what do you mean "Spark versions of the tools"... any link or example?
The Spark tools are documented in the tool docs.
When I use --native-pair-hmm-threads as 16, I know that 16 threads will be used for pair HMM calculation. What was -nct doing in the previous versions then (which step of haplotypecaller was it making fast), before it was removed in the new version?
I hope this article will help.