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ReadDepth is an R package to detect copy number variation (CNV) in short-read sequencing data. The ReadDepth algorithm uses a statistical model to account for overdispersed data and does not need reference sample data.


Genetics; genetic variation


  • Operation: Variation detection
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Apache License, Version 2.0
  • Cost: Free
  • Version name:
  • Maturity: Stable
  • Credit: The National Institutes of Health (NIH), the National Human Genome Research Institute, the National Cancer Institute, the NIH Epigenomics Roadmap Initiative, the National Institute on Drug Addiction.
  • Contact: Aleksandar Milosavljevic amilosav _at_
  • Collection: -


Miller CA, Hampton O, Coarfa C, Milosavljevic A "ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads." PLoS One. 2011 Jan 31;6(1):e16327.
PMID: 21305028
PMCID: PMC3031566

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