Control-FREEC protocols

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Control-FREEC specifications

Information


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

 (15)
2018
PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] candidate mirnas were considered to be differentially-regulated if they presented a fold change >  = 2, p-values < 0.05 and fdr less than 0.05., copy-number variants (cnv) were predicted using control-freec ver 8.0, calculating variant changes by exon and using a breakpoint threshold of 1.5. translocations were assessed using delly, using standard parameters., msi status was infered […]

2018
PMCID: 5833787
PMID: 29358619
DOI: 10.1038/s41389-017-0018-2

[…] of putative somatic mutations from previous genome-wide screenings in various cancer types was retrieved from cosmic, release v79., 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 […]

2017
PMCID: 5324064
PMID: 28233860
DOI: 10.1038/srep43469

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

2017
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 […]

2017
PMCID: 5427499
PMID: 28292787
DOI: 10.1534/g3.117.040105

[…] network analyses in splitstree, version 4.14.1 () as well as the previously reported low levels of snp diversity (figure s2 in file s2, and )., to detect and quantify cn variants we used control-freec, version 9.1 (, ), which we chose because of its low false positive rate, and high true positive rate (). importantly, the average depth of coverage or read depth of the 132 strains […]


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Control-FREEC in publications

 (56)
PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] 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 […]

PMCID: 5832318
PMID: 29494651
DOI: 10.1371/journal.pone.0193689

[…] normalized read counts across the 21 control wbcs was calculated and bins with median values > 1.4 or < 0.6 were flagged as problematic regions, potentially leading to false positive calls., control-freec (control-free copy number caller) software was used to obtain copy-number calls, using the mode without control sample []. read counts were corrected by gc content and mappability […]

PMCID: 5832792
PMID: 29497050
DOI: 10.1038/s41467-018-03276-y

[…] be identified by detecting germline mutations and comparing with cgc database with in-house software, which were presented in supplementary table ., 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 […]

PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] candidate mirnas were considered to be differentially-regulated if they presented a fold change >  = 2, p-values < 0.05 and fdr less than 0.05., copy-number variants (cnv) were predicted using control-freec ver 8.0, calculating variant changes by exon and using a breakpoint threshold of 1.5. translocations were assessed using delly, using standard parameters., msi status was infered […]

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

[…] (mb) with a median of 3.2 variants/mb, which is comparable to the mutation range detected in human bladder tumors by the tcga consortium (median = 5.5 variants/mb) []. wes data were analyzed using control-freec [], showing no major chromosomal copy number alteration (cna), nor consistent focal indel at known cancer-related loci across tumors (fig. and supplementary figures and ). […]


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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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Mike_D

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