Control-FREEC statistics

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Control-FREEC specifications


Unique identifier OMICS_00344
Name Control-FREEC
Alternative names Control-FREE Copy number and allelic content caller, Control-FREEC
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




No version available



  • person_outline Valentina Boeva

Publications for Control-FREE Copy number and allelic content caller

Control-FREEC citations


Xome Blender: A novel cancer genome simulator

PLoS One
PMCID: 5886411
PMID: 29621252
DOI: 10.1371/journal.pone.0194472

[…] . The results are provided in tab-separated format. The third function is optional and allows segmentation using CBS [] as implemented in the R-package CGHcall 2.22.0 [], and plotting of the results. Control-FREEC takes as an input aligned reads, then constructs and normalizes the copy number profile, constructs the BAF profile, segments both profiles, ascribes the genotype status to each segment […]


Integrated Molecular Characterization of Gastrointestinal Stromal Tumors (GIST) Harboring the Rare D842V Mutation in PDGFRA Gene

Int J Mol Sci
PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] t the alteration effects of on protein function and stability.Moreover, on paired tumor/normal WES data, the analysis of amplifications and large deletions was performed applying two different tools, Control FREEC v7.2 [] and ADTEX v2.0 []. A consensus method was implemented with the aim of selecting the overlapping regions given by the two algorithms (overlap of gain or loss ≥ 80%) followed by a […]


Whole exome sequencing reveals the origin and evolution of hepato cholangiocarcinoma

Nat Commun
PMCID: 5832792
PMID: 29497050
DOI: 10.1038/s41467-018-03276-y
call_split See protocol

[…] We identified copy number variants (CNVs) with control-FREEC based on exome-sequencing data to analyze the copy number state of each tumor. Control-FREEC could construct copy number profiles with aligned BAM data. Then, the profiles were normalize […]


A Carcinogen induced mouse model recapitulates the molecular alterations of human muscle invasive bladder cancer

PMCID: 5886988
PMID: 29367767
DOI: 10.1038/s41388-017-0099-6

[…] bcftools [] (ver-1.2), and then annotated using SnpEff [] (ver-4.1). Germline polymorphisms from the dbSNP build146 were removed. Copy number alterations were estimated based on the WES outputs using Control-FREEC []. Pathway enrichment analyses were performed using topGO [] (ver-2.24.0.) or ReactomePA [] against a universe gene list from mm10 Ensembl release-75. […]


Novel therapeutic strategy for cervical cancer harboring FGFR3 TACC3 fusions

PMCID: 5833787
PMID: 29358619
DOI: 10.1038/s41389-017-0018-2
call_split See protocol

[…] We sought putative somatic copy number alterations by using Control-FREEC software. The read counts per region covered by consecutive capture probes were normalized by GC content. We excluded the regions with low mappability scores calculated for the read leng […]


3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

Nat Commun
PMCID: 5715138
PMID: 29203764
DOI: 10.1038/s41467-017-01793-w

[…] CNVs were called by the Control-FREEC software at 40-kb and 500-kb resolution. Uniquely-mapped reads of the WGS dataset or Hi-C data sets were used as inputs. The ploidy parameter for RPMI-8226 and U266 cells was set to 3 an […]


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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.