CNVnator statistics

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CNVnator specifications


Unique identifier OMICS_00343
Name CNVnator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 0.3.3
Stability Stable
Maintained Yes




No version available



  • person_outline Mark Gerstein
  • person_outline Alexej Abyzov

Publication for CNVnator

CNVnator citations


A genome wide survey of mutations in the Jurkat cell line

BMC Genomics
PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] pe of sequence information to identify specific categories of variants. Our variant caller suite consisted of four distinct tools and algorithms: The Genome Analysis Toolkit, Pindel, BreakDancer, and CNVnator [–].The Genome Analysis Toolkit (GATK) from the Broad Institute uses De Bruijn graph-based models to identify single-nucleotide substitutions and small insertions and deletions. Pindel’s spli […]


Population size changes and selection drive patterns of parallel evolution in a host–virus system

Nat Commun
PMCID: 5923231
PMID: 29703896
DOI: 10.1038/s41467-018-03990-7

[…] n coevolved or evolved (as factor) with impact class (as factor) was significant by comparing a binomial GLM with the interaction and without the interaction.In order to identify copy number, we used CNVnator (URL: with 1 kb sliding windows. We identified regions with significant copy number change by comparing copy numbers of each clone in every replicate po […]


Rapid whole genome sequencing decreases infant morbidity and cost of hospitalization

PMCID: 5884823
PMID: 29644095
DOI: 10.1038/s41525-018-0049-4
call_split See protocol

[…] and mapped to genetic diagnoses., Trio blood samples were obtained where possible. rWGS was performed to ~45-fold coverage as previously described., Structural variants were identified with Manta and CNVnator, a combination that provided the highest sensitivity and precision on 21 samples with known structural variants., Structural variants were filtered to retain those affecting coding regions of […]


AMYCNE: Confident copy number assessment using whole genome sequencing data

PLoS One
PMCID: 5868770
PMID: 29579039
DOI: 10.1371/journal.pone.0189710

[…] AMY1 copy number of 86 individual samples. These estimates were compared to ddPCR results, as well as two WGS analysis methods, namely the diploid copy number estimation (DCNE) of AMY1 method [] and CNVnator []. Additionally, we analyzed the copy numbers of FCGR3A and FCGR3B in data available from 164 individuals that had been whole genome sequenced through the 1000 genomes project and genotyped […]


FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

Genome Biol
PMCID: 5859555
PMID: 29559002
DOI: 10.1186/s13059-018-1404-6

[…] aSV as the next best method (32%), followed by BreakDancer, BreakSeq2, LUMPY, DELLY, and Hydra (all near 20%).Fig. 4For duplication calls, GenomeSTRiP performed at 26% precision and 14% recall, while CNVnator performed at 22% precision and 3% recall. The MetaSV duplication calls were excluded due to the low quality VCF flag (only single caller support). FusorSV had higher recall, F-measure, and Ja […]


A randomized approach to speed up the analysis of large scale read count data in the application of CNV detection

BMC Bioinformatics
PMCID: 5831535
PMID: 29490610
DOI: 10.1186/s12859-018-2077-6

[…] ed the relative accuracy of R-GENSENG for CNV calling. We had evaluated previously the accuracy of GENSENG using the same data [, ] and compared GENSENG to the best performing read-count-based method CNVnator []. We found that GENSENG had a sensitivity of 50% averaged over the three samples, which is better than CNVnator (10% higher sensitivity and comparable specificity) []. In this study, we use […]


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CNVnator institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Psychiatry and Behavioral Sciences, School of Medicine, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Yale University, New Haven, CT, USA
CNVnator funding source(s)
Supported by the NIH and from the AL Williams Professorship funds; by the Yale University Biomedical High-Performance Computing Center, its support team, and NIH grant RR19895.

CNVnator review

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Anonymous user #12123's avatar image No country

Anonymous user #12123

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hi! I have a problerm in using this tool, hope for your help!!!
it's an error in cnvnator -root -partition
the error file is very big and for example like this:
Abnormal range (0, -1)
Abnormal range (1, 0)
Abnormal range (2, 1)
Abnormal range (3, 2)
Abnormal range (4, 3)
Abnormal range (5, 4)
Abnormal range (6, 5)
Abnormal range (7, 6)
Abnormal range (9, 8)
Abnormal range (10, 9)