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MGP-HMM is a tool for detecting copy number variation (CNV). The MGP-HMM algorithm uses a hidden Markov Model (HMM) to discriminate copies from duplicated in tandem from other repeats and, also, a Poisson distribution to model the read depth and to estimate CNV lengths.


Genetics; Genetic variation


  • Operation: Variant detection; Copy number estimation
  • Software interface: Command-line user interface
  • Language: Matlab
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: The School of Biological Sciences at Institute for Research in Fundamental Sciences, Tehran.
  • Contact: pezeshk _at_ | sadeghi _at_
  • Collection: -


Malekpour SA, Pezeshk H, Sadeghi M "MGP-HMM: Detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts." Math Biosci. 2016 Sep;279:53-62. 16.
PMID: 27424951

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