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Control-FREEC is a tool for detection of copy number variation (CNV) and allelic imbalances (LOH) in deep-sequencing data. Control-FREEC algorithm normalizes CNV and beta allele frequencies whereafter it assigns CNVs and LOH. Control-FREEC can use mappability files generated by the GEM tool.
Alternative name: FREEC.


DNA structural variation; Oncology; Human genetics


  • Operation: Genetic variation analysis
  • Input: SAM, BAM SAMtools pileup, .gz
  • Output: BAF, gain, loss, LOH, normalized CNV
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; (Microsoft Windows)
  • License: Not stated
  • Cost: Free
  • Version name: 11.5 (Windows 32 bit v5.6)
  • Credit: The Ligue Nationale contre le Cancer.
  • Contact: valentina.boeva _at_;carinogurjao _at_
  • Collection: -


Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E "Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization." Bioinformatics. 2011 Jan 15;27(2):268-9.
PMID: 21081509
PMCID: PMC3018818

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