Copy number variation detection tools within exome sequencing

Question

[mangfu100]

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?

Answer 1

[Garan]

We use ExomeDepth ( http://cran.r-project.org/web/packages/ExomeDepth/index.html ) and CoNVeX ( http://www.biomedcentral.com/1471-2105/14/S2/S2 ) 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.

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