Running HaplotypeCaller with -nct

louws

Hi!
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.

Geraldine_VdAuwera

Hi there,

Gains from multithreading can be highly variable depending on platform. If that's not working well for you, there are other things you can try. You can parallelize using scatter-gather, and you can do things like limit the number of alternate alleles the program will consider, or tweak the graph pruning argument. These have been covered on this forum and in the documentation; try doing a search for terms like pruning and scatter-gather.

Geraldine_VdAuwera

Hi there,

Gains from multithreading can be highly variable depending on platform. If that's not working well for you, there are other things you can try. You can parallelize using scatter-gather, and you can do things like limit the number of alternate alleles the program will consider, or tweak the graph pruning argument. These have been covered on this forum and in the documentation; try doing a search for terms like pruning and scatter-gather.

louws

Thank you Geraldine, I will investigate all the above mentioned options, especially regarding the scatter-gather option.