Parallelisation of CreateRecalibrationTable

SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

https://nf-co.re/sarek

MIT License

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Closed kokyriakidis closed 4 years ago

kokyriakidis commented 5 years ago

Hello, Since I saw this step uses only on core on my 20 core system, I searched on GATK forum and found this:

https://gatkforums.broadinstitute.org/gatk/discussion/23453/gatk4-baserecalibrator-multithreading-not-spark

Do you think it could be something you could implement?

maxulysse commented 5 years ago

That does seems interesting. I'll look into it.

maxulysse commented 5 years ago

You can try https://github.com/MaxUlysse/Sarek/tree/ParallelizeMore That should be a good start in improving all that

maxulysse commented 4 years ago