Recommended by Illumina, ONCOCNV is a package to detect copy number changes in Deep Sequencing data developed by OncoDNA with the collaboration with the Bioinformatics Laboratory of Institut Curie (Paris).

ONCOCNV automatically computes, normalizes, segments copy number profiles then calls copy number alterations. The user can provide any positive number of control samples in order to construct the baseline. However, we recommend using at least three control samples.

Note: ONCOCNV can be applied to exome-seq data. You just need to provide probe coordinates instead of amplicon coordinates, and you will get beautiful copy number profiles for your data.

For more detailed information, please refer to the OncoCNV publication: http://bioinformatics.oxfordjournals.org/content/30/24/3443.long