Hi.

I would like to search copy number variation using exome sequence data.

I have been using VarScan2 to detect copy number variations.

However, I am looking for more well-known or advanced variation in detecting copy number.

Can you suggest well-known and the most popular copy number variation tools within exome sequencing?
<p>We use ExomeDepth ( <a href="http://cran.r-project.org/web/packages/ExomeDepth/index.html">http://cran.r-project.org/web/packages/ExomeDepth/index.html</a> ) and CoNVeX ( <a href="http://www.biomedcentral.com/1471-2105/14/S2/S2">http://www.biomedcentral.com/1471-2105/14/S2/S2 </a>) for copy number detection on targeted NGS panels (custom panel with bait density varied by depth of coverage from exome sequencing data), both have their pros and cons - with CoNVeX seemingly more susceptible to batch effects if there is alot of variation between samples.</p>

<p>We also use CoNVeX on whole exome data although you do get alot of false positives due to the high variablity in coverage.</p>
