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CNVkit is a tool for detection and visualization of copy number variation (CNV). The algorithm uses targeted and off-target sequence reads for the inference of CNV.


DNA structural variation


  • Operation: Variant calling
  • Software interface: Library
  • Language: Python
  • Operating system: Linux; Mac OS X
  • License: Apache License v2
  • Cost: Free
  • Version name: -
  • Maturity: Mature
  • Credit: The National Institutes of Health [R01 CA131524, P01 CA025874 to BCB].
  • Contact: boris.bastian _at_
  • Collection: -


Talevich E, Shain AH, Botton T, Bastian BC "CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing." PLoS Comput Biol. 2016 Apr 21;12(4):e1004873.
PMID: 27100738
PMCID: PMC4839673

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