Hi,
I have exome sequencing data from cases and controls and looking to conduct a case-control study to find copy number variations (CNVs) associated with a disease. I have been looking into CNV calling algorithms for exome sequencing data and was wondering if there is a good guide on how to do this? I found several CNV detection algorithms such as ExomeDepth, GATK gCNV, Lumpy, DELLY, and cn.MOPS . The question that I have, which ones have the best performance or are highly recommended?
Your help is greatly appreciated!
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