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Contra is a tool to detect copy number variation (CNV) from targeted resequencing data. It reports gains and losses in respect to a normalized depth of coverage.


Genomics; Sequencing; Oncology; DNA structural variation


  • Operation: Sequence analysis; Polymorphism detection; Copy number estimation; Structural variation detection
  • Input: BAM; SAM
  • Output: variant call format (VCF4.0)
  • Software interface: Command-line user interface
  • Language: R;Python
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 2.0.8
  • Maturity: Mature
  • Credit: Peter MacCallum Cancer Foundation Endowment Fund, the Victorian Breast Cancer Research Consortium and Australian Research Council (grant DP1096296).
  • Contact: _at_;richard.lupat _at_
  • Collection: -


Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, Ryland GL, Tothill RW, Halgamuge SK, Campbell IG, Gorringe KL "CONTRA: copy number analysis for targeted resequencing." Bioinformatics. 2012 May 15;28(10):1307-13.
PMID: 22474122
PMCID: PMC3348560

Hooghe B, Hulpiau P, van Roy F, De Bleser P "ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species." Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W128-32. 10.1093/nar/gkn195. Epub 2008 May 3.
PMID: 18453628
PMCID: PMC2447729

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