I was wondering what are some of the popular CNV detection tools from NGS data? I am looking for ones that can also detect aneuploidy.
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.
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.