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Illumina / strelka

Strelka2 germline and somatic small variant caller
GNU General Public License v3.0
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--callRegions for WGS - run in parallel for i.e. each Chromosome #206

Closed FriederikeHanssen closed 2 years ago

FriederikeHanssen commented 2 years ago

Thank you for providing this tool. I have searched the issues and docmentaiton but couldn't find an answer to my question. So apologies if that is already answered elsewhere and I missed it.

Is it possible to run Strelka2 (v 2.9.10) in parallel for each region for one patient, such as one run for chr1, one for chr2 and so on and merge the resulting vcfs in the end?

Thank you :)

sagitaninta commented 2 years ago

I think this is what already happen when you run ${runningDirectory}/runWorkflow.py -m local -j 20. See https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#execution

Hope this helps.

FriederikeHanssen commented 2 years ago

somewhat, yes.