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

Detail

  • Operation: Genetic variation analysis

  • Software interface: Command-line user interface

  • Language: C++

  • License: -

  • Cost: Free

  • Version name: 11.5 (Windows 32 bit v5.6)

  • Credit: The Ligue Nationale contre le Cancer.

  • Input: SAM, BAM SAMtools pileup, .gz

  • Output: BAF, gain, loss, LOH, normalized CNV

  • Contact: valentina.boeva@inserm.fr;carinogurjao@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
  • Boeva V, et al. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. 2011; 27:268-9. doi: 10.1093/bioinformatics/btq635
  • https://doi.org/10.1093/bioinformatics/btq635
  • PMID: 21081509
  • PMC: PMC3018818

Download and documentation

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