I would like to check the presence of germline CNV in my samples. I wonder what are the best germline CNV callers using WES data ? Please share your experiances
Thanks in advance
We've used XHMM. It works with DepthOfCoverage data generated using GATK.
Thanks! isn't it difficult to run?
Is it? I think Menachem pretty much walks you through the entire process in the manual.