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cn.mops (Copy Number estimation by a Mixture Of PoissonS) is an R package pipeline for analysis of copy number variation (CNV) in next-generation sequencing (NGS) data. The cn.mops pipeline contains a function for conversion of BAM files into read count matrices and genomic ranges. The algorithm uses Bayesian and Poisson statistics to model the depth coverage and filter out noise.


Sequencing; Molecular genetics


  • Operation: Variation detection; Copy number estimation
  • Input: BAM, Read count matrices
  • Output: -
  • Software interface: Command-line user interface; Library
  • Language: R;C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.30.0
  • Maturity: Stable
  • Credit: The Institute of Bioinformatics, Johannes Kepler University Linz.
  • Contact: cn.mops _at_
  • Collection: BioConductor


Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, Hochreiter S "cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate." Nucleic Acids Res. 2012 May;40(9):e69.
PMID: 22302147
PMCID: PMC3351174

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21.
PMID: 25633503
PMCID: PMC4509590

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.
PMID: 15461798
PMCID: PMC545600

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