CNVtools protocols

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CNVtools specifications


Unique identifier OMICS_02090
Name CNVtools
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.74.0
Stability Stable
R(>=2.10), survival
Maintained Yes


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  • person_outline Chris Barnes <>

Publication for CNVtools

CNVtools in pipelines

PMCID: 5883389
PMID: 29682616
DOI: 10.21956/wellcomeopenres.15113.r31105

[…] samples (figure 1) is impressive. the clustering of the results from the uk biobank samples is also very clear, validating the precision and accuracy of the gaussian mixture models extracted by cnvtools., for the gene expression analyses at the rna level i would agree with the conclusions stated in the first paragraph of the discussion, that although the transcription level for ccl3l1 […]

PMCID: 4702374
PMID: 26739746
DOI: 10.1186/s13073-015-0255-y

[…] 2 (feb 2009) and 1000 genomes pilot 1 ceu (march 2010) []. full details are provided in the additional file ., a suite of perl and r (2009) scripts were used as a framework to utilise the r package cnvtools, available from []. all the steps are detailed in the additional file ., genotyping of rs112942398 was performed […]

CNVtools in publications

PMCID: 5937907
PMID: 29675612
DOI: 10.1007/s00439-018-1883-2

[…] taken to represent copy number, and normalised so that the standard deviation of the data was 1. for each cohort, a gaussian mixture model of four or five components was fitted to the data using the cnvtools software implemented in the statistical language r v.3.2.3, with each component representing a integer copy number class (barnes et al. ). samples were then assigned to each component […]

PMCID: 5883389
PMID: 29682616
DOI: 10.21956/wellcomeopenres.15113.r31105

[…] as previously , . the copy number values clustered about integer copy numbers, and a gaussian mixture model was fitted to allow assignment of individuals to an integer copy number call using cnvtools . for the 5000 individuals from uk biobank, 58 individuals were selected by uk biobank investigators as blind spiked duplicates as part of the quality control check to ensure genotyping […]

PMCID: 5320550
PMID: 28225073
DOI: 10.1038/srep43178

[…] are further identified, and refined to ensure qualified copy number variant calls. the second step is to determine the discrete copy numbers for each cnv locus from the probe-level intensity data. cnvtools and a two-dimensional model (gaussian mixture), are used to infer the copy numbers from the maximum posterior likelihood function. a meta-approach combining the two algorithms […]

PMCID: 5363352
PMID: 27995740
DOI: 10.1002/humu.23159

[…] ratio data from agilent 2×105k acgh experiments were used [conrad et al., ; craddock et al., ]. including technical duplicates, a total of 21,858 acgh experiments were analyzed using the software cnvtools 1.42.3 [barnes et al., ] implemented in r v.3.1.1 [the r development team, ]. briefly, the first principal component (pc) of the data is fitted to a gaussian mixture model, with three […]

PMCID: 5287127
PMID: 28154514
DOI: 10.5808/GI.2016.14.4.216

[…] to discover cnv regions, we employed cnvs that were called in over three individuals []., cnv genotypes consist of zero copies, one copy, and two copies. to do this, we used an r package, named ‘cnvtools,’ with default parameters to estimate cnv genotypes []. cnvtools is a mixture model for one-dimensional cnv data summary that can separate samples into each cnv genotype. to estimate […]

CNVtools institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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