CNV-seq statistics

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CNV-seq specifications


Unique identifier OMICS_00339
Name CNV-seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Aligned read positions
Operating system Unix/Linux, Mac OS
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


Publication for CNV-seq

CNV-seq citations


Pain correlates with germline mutation in schwannomatosis

PMCID: 5805424
PMID: 29384852
DOI: 10.1097/MD.0000000000009717

[…] either nonsense or deleterious missense (as predicted by in silico analysis or previous rna studies), and were confirmed by sanger sequencing analysis using an abi prism 3730 dna analyzer. we used cnv-seq to call copy-number variations on intragenic regions of 5 target genes from capture-sequencing data []. we compared 30 subjects with schwannomatosis to an equal number of subjects with nf1 […]


Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry

Genome Biol Evol
PMCID: 5737360
PMID: 29048530
DOI: 10.1093/gbe/evx199

[…] using in-house scripts. raw reads were then mapped to the reference assembly using nextgenmap (). sample coverages computed by gatk can be found in , online. copy number variation was assessed with cnv-seq using default parameters (). a gene was considered to have copy number variation if a cnv-seq window with a significant signature of copy number variation intersected an exon of the gene […]


Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage

PMCID: 5596349
PMID: 28900023
DOI: 10.1128/mBio.01393-17

[…] transmembrane genes in the genome [p < 0.05]) download table s4, pdf file, 0.03 mb., differentially expressed genes in the 4 largest cnv regions identified in the ackerman-k26 comparison based on cnv-seq (tthere were a total of 10 genes in cnvr114 [chromosome 24], 11 genes in cnvr181 [chromosome 11], 14 genes in cnvr159-178 [chromosome 27], and 11 in cnvr240 [chromosome 23]; the cnv region […]


Use of next generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia[S]

J Lipid Res
PMCID: 5665663
PMID: 28874442
DOI: 10.1194/jlr.D079301

[…] data has been investigated previously; however, it remains a relatively new and challenging field. commonly used cnv prediction programs include conifer (), exomedepth (), exomecopy (), xhmm (), and cnv-seq (); however, many of these designated methods have shown high rates of false-positive cnvs, which poses a major limitation on potential clinical use. moreover, many of the literature-reported […]


A Total variation Constrained Permutation Model for Revealing Common Copy Number Patterns

Sci Rep
PMCID: 5575355
PMID: 28851906
DOI: 10.1038/s41598-017-09139-8

[…] (control-free copy number and allelic content caller) uses least absolute shrinkage and selection operator (lasso) regression to identify the breakpoint and detects copy number profiles. cnv-seq (copy number variation using shotgun sequencing) uses a gaussian distribution to model read depth signal. cnaseg (copy number abnormality segmentation) employs a hidden markov model(hmm) […]


Whole genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds

PLoS One
PMCID: 5571935
PMID: 28841720
DOI: 10.1371/journal.pone.0183921

[…] in the present study, for identifying small indels, the lenghth of 1 to 3 bp indels were obtained by setting relevant parameters., the cnvs calls on the cattle genomes were identified using the cnv-seq program. briefly, the nanyang and qinchuan reads were mapped to the bos_taurus_umd_3.1 using the bwa, and the output of bam was converted into the "best-hit" format required by cnv-seq using […]

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CNV-seq institution(s)
Department of Biological Sciences, National University of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore; Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
CNV-seq funding source(s)
Supported by National University of Singapore FRC grant number R154000265112 and a National University of Singapore Research Scholarship.

CNV-seq review

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Antoine Rousselin

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I have been using this tool since 2009 for the detection of CNV in genes predisposed to breast and ovarian cancer. After having modified a little original script, adapt the parameters this software is very precise (specificity, sensitivity). But it is not suitable for analysis on a large panel of genes.