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CNVer specifications

Information


Unique identifier OMICS_00341
Name CNVer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.8.1
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Wang Y.P. <>
  • person_outline CNVer Team <>

Publication for CNVer

CNVer in publications

 (6)
PMCID: 5056704
PMID: 27723766
DOI: 10.1371/journal.pone.0164212

[…] calls; all samples had a variant concordance higher than 99.5%., in order to achieve high-confidence structural variants calls for our samples, two different algorithms were used. the first one, cnver v0.8.1[], uses information from the paired-end mappings and from the depth of coverage in a given region to call cnvs (insertions and deletions). prior to the mapping, the fastqmcf v1.1.2 […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] svs have been reported., combining rc for the detection of large events and rp for accurate identification of breakpoints can reduce the number of false positive calls [svdetect (zeitouni et al., ), cnver (medvedev et al., ), gasvpro (sindi et al., ), and ingap-sv (qi and zhao, )]. genome strip (handsaker et al., ) exploits rp, rc, sr, and population-scale patterns to detect genome structural […]

PMCID: 4374778
PMID: 25812131
DOI: 10.1371/journal.pone.0122287

[…] diagrams were generated to show the agreement between the different algorithms, before and after filtering out familial inconsistencies. this filtering revealed a high number of false positives for cnver and breakdancer. a low overall agreement between the methods suggested a high complementarity of the different tools when calling cnvs. the breakpoint sensitivity analysis indicated […]

PMCID: 3604020
PMID: 23527109
DOI: 10.1371/journal.pone.0059128

[…] were excluded because of stability issue. from the same dataset, there were issues getting the code to fully perform to our expectations. our study focused on the method with doc signature, so cnver and copyseq were excluded because they combine both roc and pem signature. a comparison between the combined signature based methods with the single signature based methods can be found in . […]

PMCID: 3490498
PMID: 23139896
DOI: 10.3390/genes3030545

[…] [], we have implemented some workflows, as a first wave of a more comprehensive set of tools. among the many different approaches to call cnvs, we have chosen the three approaches described in ., cnver relies both on read depth and read pair information [] in a computational framework called the donor graph, that reduces the sequencing biases causing uneven local coverage (). […]


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CNVer institution(s)
Department of Biomedical Engineering, Tulane University, New Orleans, LA, USA; Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
CNVer funding source(s)
Supported by the National Institutes of Health and National Science Foundation.

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