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What are the step for germline analysis with CNVKit?

Hello,

I would like to call CNV on germline samples with CNVKit. the documentation for CNV calling from germline is a bit confusing. could you please give me a step by step instruction to run CNVkit on germline WES data?

Thanks sara

whole exome sequneing
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written by jonessara770 jonessara770

I see you've given up on XHMM already :-)

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written by Ram Ram

No, I would like to try some of them and compare the results. XHMM installation is very difficult!

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written by jonessara770 jonessara770

Oh I see. We have an HPC where it's installed, but I guess installation from scratch might be difficult. No docker images?

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written by Ram Ram

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