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PICNIC is a software tool to predict copy number variation (CNV) in microarray cancer data. The PICNIC algorithm uses a unique preprocessing transformation and a hidden Markov Model (HMM) which is specific to cancer data. It classifies genotypes, specifies regions of loss of heterozygosity (LOH), and produces allelic copy number segmentation.


Genetics; Oncology; Genetic variation


  • Operation: Variant detection; Copy number estimation
  • Software interface: Command-line user interface; graphical user interface
  • Language: Perl;Java
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: CGP Software License
  • Cost: Free
  • Version name: -
  • Maturity: Legacy
  • Credit: The Wellcome Trust.
  • Contact: cgpit _at_
  • Collection: -


Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D, Swamy S, Santarius T, Chen L, Widaa S, Futreal PA, Stratton MR "PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data." Biostatistics. 2010 Jan;11(1):164-75. 2009 Oct 15.
PMID: 19837654
PMCID: PMC2800165

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