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CoNVaDING specifications

Information


Unique identifier OMICS_29312
Name CoNVaDING
Alternative name Copy Number Variation Detection In Next-generation sequencing Gene panels
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2.1
Stability Stable
Requirements
Statistics::normality package, Samtools
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Lennart Johansson
  • person_outline Freerk van Dijk

Publication for Copy Number Variation Detection In Next-generation sequencing Gene panels

CoNVaDING citations

 (3)
call_split

Combining targeted panel based resequencing and copy number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies

2018
Sci Rep
PMCID: 5869593
PMID: 29588463
DOI: 10.1038/s41598-018-23520-1
call_split See protocol

[…] eviously detected by genotyping microarray (Supplementary Table ). All variants used as controls were correctly identified.A CNV analysis was performed with NGS data following the previously reported CoNVaDING method, which had been specifically developed for gene panel data at high-coverage and enables accurately single-exon detection. Briefly, it uses the average coverage of each specified targe […]

call_split

Assessment of the incorporation of CNV surveillance into gene panel next generation sequencing testing for inherited retinal diseases

2017
J Med Genet
PMCID: 5800348
PMID: 29074561
DOI: 10.1136/jmedgenet-2017-104791
call_split See protocol

[…] (). Events that were analysed in a clinical context were all (1) identified against three independent reference sets using ExomeDepth, (2) identified by at least one other CNV software tool (CoNVex, CoNVaDING or both) and (3) visually inspected using the ExomeDepth graphical package.We first limited our analysis of CNV events to those that had been identified by ExomeDepth in comparison to three […]

library_books

panelcn.MOPS: Copy‐number detection in targeted NGS panel data for clinical diagnostics

2017
Hum Mutat
PMCID: 5518446
PMID: 28449315
DOI: 10.1002/humu.23237

[…] We compared panelcn.MOPS against the following five state‐of‐the art methods for CNV detection in NGS panel data: ExomeDepth version 1.1.8, CoNVaDING version 1.1.6, VisCap, NextGENe version 2.4.1.1, and SeqNext version 4.3.0. Details about the methods, including the parameters that were optimized on the validation set, can be found in Sup […]

Citations

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CoNVaDING institution(s)
University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
CoNVaDING funding source(s)
Supported by The Netherlands CardioVascular Research Initiative (CVON2011-19; Genius).

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