Cnvkit suits WES data, gatk can handle both WES and WGS data.

There are too many CNV detection tools. For WES and WGS, I use Control FREEC, which works for paired (i.e., with a test and normal / reference sample) or unpaired analyses.

Kevin

If you are working with gene panels, DECoN and panelcn.mops work quite well too. They are tuned to detect indels affecting a few exons or a gene and work best in germline.