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GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Question and suggestion re -nct & -num_threads options

Member

Hi,

I'm trying to implement a workflow with GATK for the first time and I'm getting caught out by the -nct/-num_threads options not being compatible with all walkers, erroring and then killing the process.

Can I suggest that if the flags are not implemented/supported by a walker that the option is ignored. The docs don't clarify which walkers work and which don't so I need to test each one. It would be much easier if simply a warning message were given.

Also, I don't fully understand the difference between -nct/-num_threads. Can someone explain it, please?
TIA

Tagged:

• Member

It's a shame the -nct option can't be ignored if not (yet) implemented.

Thanks for the clarification and I'll look forward to the new documentation.

• Member

Hey,

I'm also very interested in that documentation. Any news about that?

Best regards

• Member

Me too. Looking forward to that documentation. Thanks GATK team!