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Optimize CPU for Manta #77

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Faizal-Eeman opened this issue Oct 24, 2022 · 2 comments
Open

Optimize CPU for Manta #77

Faizal-Eeman opened this issue Oct 24, 2022 · 2 comments
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@Faizal-Eeman
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    Manta has a parallelization option with `-j` to make use of multiple cores; it'd be good to explore increasing the number of CPUs for optimization. See call-sSNV Strelka-2 workflow for an example.

Originally posted by @yashpatel6 in #74 (comment)

@tyamaguchi-ucla
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Not sure how effective this change would be for SV calling but it took 5-7 days for Manta to call SVs in large WGS samples (400-600GB normal/tumor BAMs) using v6.1.0.

@tyamaguchi-ucla
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@Faizal-Eeman See https://github.com/uclahs-cds/pipeline-call-sSNV/blob/772592a2e11672a4901ef90f8f45978e4ea9bbae/module/strelka2-processes.nf#L52

We've done extensive benchmarking in call-sSNV. We should check it out and see if we can apply the result to this pipeline and call-gSV.

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