Speeding up snp variant calling?

epi2me-labs / wf-human-variation

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Speeding up snp variant calling? #148

Closed Krysasp closed 4 months ago

Krysasp commented 4 months ago

Ask away!

Hi there. Is there anyway to run the subprocess of Clair3 variant caller, 'CallVariantsFromCffi ' in parallel or allocating more chuncks to speed it up? I noticed there isn't an option to multi-thread it, only python Clair3 does.. the snp calling using Cffi progresses slow on my local cluster. ...

SamStudio8 commented 4 months ago

wf-human-variation already parallelises the CallVariantsFromCffi steps across all chunks generated by Clair3. If you are seeing performance issues with wf-human-variation on your cluster, please can you provide more information by opening a Bug report for us to take a look.