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?
I see you've given up on XHMM already :-)
No, I would like to try some of them and compare the results. XHMM installation is very difficult!
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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