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ONCOCNV is a tool to detect copy number variation (CNV) in ultra-deep targeted sequencing. The algorithm uses multifactor normalization and annotation techniques to detect large copy number variation in amplicon sequencing data. The Authors claim their method to have comparable precision to CGH techniques.


DNA; Sequencing; Data quality management


  • Operation: Standardisation and normalisation; variation detection
  • Input: BAM
  • Output: Annotation of genes with copy number changes + visualization of the profile (.png)
  • Software interface: Command-line user interface
  • Language: R;Perl
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 6.9
  • Maturity: Mature
  • Credit: Agence Nationale de le Recherche (Investissements d’avenir) and SiRIC (Site de Recherche Intégré sur le Cancer), he NGS platform of the Institut Curie, Agence Nationale de la Recherche (Investissements d’avenir) and by the Canceropôle Ile-de-France.
  • Contact: infos _at_;valentina.boeva _at_
  • Collection: -


Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Rio Frio T, Hupé P, Barillot E, Laes JF "Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data." Bioinformatics. 2014 Dec 15;30(24):3443-50.
PMID: 25016581
PMCID: PMC4253825

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