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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Running PennCNV in parallel #82

Closed sophie-03 closed 1 year ago

sophie-03 commented 2 years ago

I am currently calling CNVs from SNP genotype arrays using detect_cnv.pl, I have 500,000 samples so this is taking quite a long time. Is there a way to run this in parallel to speed up the process?

kaichop commented 2 years ago

You can run in 500 threads, each with 1000 samples (put file name in a list file). This can be done rapidly if you are allowed to submit 500 jobs at the same time in your computing cluster.

On Fri, May 13, 2022 at 6:53 AM Sophie @.***> wrote:

I am currently calling CNVs from SNP genotype arrays using detect_cnv.pl, I have 500,000 samples so this is taking quite a long time. Is there a way to run this in parallel to speed up the process?

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