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I am trying to see if I can speed up the HaplotypeCaller tool using the -nct flag. The GATK correctly identifies that my machine has 16 processors, and I specified that the HaplotypeCaller uses 16 threads, i.e. -nct 16. However processing the same file roughly takes the same amount of time (3600sec approx). I tried it also using -nct 8, and -nct 4. None of these options seems to help the process finish faster.
Were there any suggestions or ways I could achieve some appreciable gains? Thank you for any insight anyhow.