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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

Versioning


No version available

Maintainers


  • person_outline Wang Y.P.
  • person_outline CNVer Team

Publication for CNVer

CNVer citations

 (6)
library_books

Paternal Age Explains a Major Portion of De Novo Germline Mutation Rate Variability in Healthy Individuals

2016
PLoS One
PMCID: 5056704
PMID: 27723766
DOI: 10.1371/journal.pone.0164212

[…] 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 (https […]

library_books

Detection of Genomic Structural Variants from Next Generation Sequencing Data

2015
Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] of 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 pol […]

library_books

Comparison of Sequencing Based CNV Discovery Methods Using Monozygotic Twin Quartets

2015
PLoS One
PMCID: 4374778
PMID: 25812131
DOI: 10.1371/journal.pone.0122287

[…] Four CNV-calling tools have been selected for comparison (CNVer, BreakDancer, CNVnator and ERDS) (). The selection of these tools was based on the differences in their underlying algorithmic approaches. At least one algorithm of each of the main categories w […]

library_books

Computational tools for copy number variation (CNV) detection using next generation sequencing data: features and perspectives

2013
BMC Bioinformatics
PMCID: 3846878
PMID: 24564169
DOI: 10.1186/1471-2105-14-S11-S1

[…] to increase the performance in detecting CNVs and reduce false positive discoveries.Five tools in Table are able to use PEM and RD information to identify CNVs in populations, including SVDetect [], CNVer [], Genome STRiP [], GASVPro [], and inGAP-sv []. As aforementioned, combinatorial methods can take advantage of the uniqueness of multiple tools and, thus, can reduce more false positives than […]

library_books

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

2012
Genes
PMCID: 3490498
PMID: 23139896
DOI: 10.3390/genes3030545

[…] cking [], 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 (). The most interest […]

library_books

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data

2011
BMC Bioinformatics
PMCID: 3194192
PMID: 21989326
DOI: 10.1186/1471-2105-12-S6-S4

[…] advantage of multiple discordant mate pairs that deviate from mean distance values consistently but less significantly than the threshold.Medvedev et al 2010 [] presented a donor graph- based method (CNVer) to infer CNVs using both mate-pair and depth-of-coverage information. The advantage of CNVer is that by using mate pair discordant and depth-of-coverage information jointly, it has better accur […]

Citations

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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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