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DupHMM is a tool for detection of copy number variation (CNV) of reads mapped to a reference genome. The DupHMM algorithm sections chromosomes into user specified window sizes and uses Poisson distribution to emit probabilities to a Hidden Markov Model (HMM) to model single copy and duplicated chromosomal regions.


Genetics; sequence analysis; genetic variation


  • Operation: Sequence analysis; Variant detection; Copy number estimation
  • Input: SAM file
  • Output: -
  • Software interface: Command-line user interface
  • Language: R;C++;Python
  • Operating system: Linux
  • License: The MIT licence
  • Cost: Free
  • Version name: -
  • Credit: -
  • Contact: mdporter _at_
  • Collection: -


Download and documentation

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