Popular CNV detection tools

Question

[Floydian_slip]

Hi, 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. Thanks!

Answer 1

[MatthewP]

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

Answer 2

[Kevin Blighe]

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

Answer 3

[bernatgel]

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.