Which tool is recommended for detecting CNVs in whole exome sequencing?
There are many tools for CNV detection but it depends on the type of your data. Some below mentioned tools list need control or normal samples and if that is not available check for the manuals on how to analyse without providing control. They are not specifically designed for whole exome sequencing but works well.
I add XHMM (http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml )