Copy number variations from WES data

Question

[shivangi.agarwal800]

Hi,

I want to derive copy number variation information from whole exome data. Please suggest which tool/pipeline should I refer?

[Kevin Blighe]

• Control-FREEC (shell)
• DNAcopy (R)

[2nelly]

I mostly use VarScan for this job. it is pretty straight forward and designed specifically for exome sequencing.

http://varscan.sourceforge.net/copy-number-calling.html

Answer 1

[Rongxin]

Hi,

Please see this paper Comparative study of whole exome sequencing-based copy number variation detection tools, which may provide you with some suggestions.