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MixHMM is a tool for inferring copy number variation (CNV) and allelic imbalance from single nucleotide polymorphism (SNP) array data. The MixHMM algorithm uses a unique hidden Markov model (HMM) for chromosomal structural aberrations as hidden states and an innovative sample mixing design to detect tumor CNV in heterogeneous samples.


Genetics; Oncology; Genetic variation


  • Operation: Variation detection; Copy number estimation
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: Not stated
  • Cost: -
  • Version name: -
  • Maturity: Legacy
  • Credit: Yale Center of Excellence in Molecular Hematology, Yale Comprehensive Cancer Center, Targeted Area of Research Excellence Award.
  • Contact: David Tuck david.tuck _at_
  • Collection: -


Liu Z, Li A, Schulz V, Chen M, Tuck D "MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells." PLoS One. 2010 Jun 1;5(6):e10909.
PMID: 20532221
PMCID: PMC2879364

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