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ExomeCNV is a tool for detection of copy number variation (CNV) and loss of heterozygosity (LOH). The algorithm uses statistics of sequence coverage and B-allele frequencies for the estimation of CNV and LOH.


Exome sequencing; Statistics and probability; Genetic variation; Sequence analysis


  • Operation: Genetic variation analysis; Sequence alignment analysis; variant detection
  • Input: BAM, Pileup, GTF
  • Output: -
  • Software interface: Command-line user interface; library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 1.4
  • Maturity: Legacy
  • Credit: National Heart, Lung, Blood Institute of the US National Institutes of Health grant (1RC2 HL101715, to J.Q.); National Institute for Mental Health (R01 MH071852); National Institute of Arthritis, Musculoskeletal and Skin Disorders (P30 AR057230); National Cancer Institute (P30 CA16042).
  • Contact: fsathira _at_; snelson _at_
  • Collection: -


Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF "Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV." Bioinformatics. 2011 Oct 1;27(19):2648-54.
PMID: 21828086
PMCID: PMC3179661

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