For better experience, turn on JavaScript!


Control-FREEC

Control-FREEC

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.

Topic

DNA structural variation; Oncology; Human genetics

Details

  • 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_ inserm.fr;carinogurjao _at_ gmail.com
  • Collection: -

Publications

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. https://doi.org/10.1093/bioinformatics/btq635
PMID: 21081509
PMCID: PMC3018818


Download and documentation








If you find errors, please report here.