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HD-CNV is a tool for identifying copy number variant (CNV) sites of interest by comparing CNVs between different samples. The algorithm finds cliques in a graph and produces spread sheet data and UCSC Genome Browser track files.


Biology; genetics; molecular genetics; genetic variation


  • Operation: Calculation; sequence composition calculation; repeat sequence organisation analysis
  • Input: CSV
  • Output: CSV; UCSC track files
  • Software interface: Command-line user interface; graphical user interface
  • Language: Java
  • Operating system: Linux; MACOS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 3
  • Maturity: Stable
  • Credit: Natural Sciences and Engineering Research Council (NSERC) of Canada.
  • Contact: jcamer7 _at_
  • Collection: -


Butler JL, Osborne Locke ME, Hill KA, Daley M "HD-CNV: hotspot detector for copy number variants." Bioinformatics. 2013 Jan 15;29(2):262-3.
PMID: 23129301

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