Control-FREEC protocols

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



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  • person_outline Valentina Boeva <>

Publications for Control-FREE Copy number and allelic content caller

Control-FREEC IN pipelines

PMCID: 5324064
PMID: 28233860
DOI: 10.1038/srep43469

[…] the genome analysis tool kit (gatk)31 was used for detecting snv and indel. the resulting variants were annotated with the annovar software32. to detect copy-number alterations (cnvs), we applied control-freec33 to the read count profiles of sequence data. analysis of structural variants (svs) was performed by crest34 using the default parameters. candidate breakpoints in tumors that also […]

PMCID: 5360271
PMID: 28323875
DOI: 10.1371/journal.pone.0174118

[…] data to the reference genome (ucsc hg19) to obtain the original mapping results. samtools was used for variant calling and the identification of single nucleotide polymorphisms and indels. control-freec was utilized for copy number variation detection, and crest was utilized for the detection of structure variant information in variant calling., annovar was utilized to annotate […]

PMCID: 5754767
PMID: 29203670
DOI: 10.1073/pnas.1708391114

[…] for recurrent pams includes ≥2 events in at least two animals. we inferred the copy number landscape of each tumor from its exome sequence and the exome sequence of its matched normal, using control-freec (36). we defined cnas as copy number (cn) gain (2.8 ≤ cn < 4), amplification (cn ≥ 4), loss (1 < cn ≤ 1.4), and deletion (cn ≤ 1), and inferred their significance using gistic2.0 […]

PMCID: 5780004
PMID: 29039585
DOI: 10.3892/mmr.2017.7805

[…] ( (22), containing large fragments of deletions, insertions, duplication and copy number variants, inversion and translocation. cnvs were identified using control-freec v6.7 software ( (23), containing deletions and duplications., genome dna was extracted from tumor tissues of four patients with lung […]

PMCID: 5192280
PMID: 28082821
DOI: 10.3748/wjg.v22.i48.10680

[…] 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 […]

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.