Control-FREEC specifications


Unique identifier OMICS_00344
Name Control-FREEC
Alternative name Control-FREE Copy number and allelic content caller
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data : Some aligned reads.
Input format SAM,BAM,Pileup,Eland,BED,SOAP,arachne,BLAT,Bowtie
Operating system Unix/Linux, Windows
Programming languages C, C++
Computer skills Advanced
Version 11.44
Stability Stable
Maintained Yes



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  • person_outline Valentina Boeva <>

Control-FREEC articles

Control-FREEC citations

PMCID: 5192280

[…] on 137 clinically relevant genes related to biological pathways linked to cancer predisposition or available targeted therapies (supplementary table 1). copy number variations were studied by using control-freec software as described[5,6]., a 58-year-old caucasian male initially presented with abdominal pain. a ct scan, carried out in june 2011, revealed a metastatic sigmoid cancer […]

PMCID: 4570720

[…] the sequences were aligned to the ncbi build 37 (hg19) reference using bwa [44] and processed following gatk best practices. the base score re-calibrated bam files were used for cna detection., control-freec was applied in this study on both wgs and wes data. it divided the genome into small contiguous regions using sliding windows. the read count profiles in each region for normal […]

Control-FREEC institution(s)
Institut Curie, Paris, France, INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris, France; Mines ParisTech, Fontainebleau, France; INSERM, U830, Genetics and Biology of Cancers, Paris, France; INRIA Saclay, Orsay, France
Control-FREEC funding source(s)
Supported by the “Projet Incitatif et Collaboratif Bioinformatique et Biostatistiques” of the Institut Curie; Ligue Nationale Contre le Cancer.

Control-FREEC review

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Works okay. Just can't seem to make it take into account the mappability files when not using matched samples.