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Protocols

CoVEC specifications

Information


Unique identifier OMICS_13232
Name CoVEC
Alternative name Consensus Variant Effect Classification
Interface Web user interface
Restrictions to use None
Input data Output scores from SIFT, PolyPhen2, SNPs&GO or Mutation Assessor
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Kimon Frousios

Information


Unique identifier OMICS_13232
Name CoVEC
Alternative name Consensus Variant Effect Classification
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Kimon Frousios

Publication for Consensus Variant Effect Classification

CoVEC citations

 (3)
library_books

High confidence assessment of functional impact of human mitochondrial non synonymous genome variations by APOGEE

2017
PLoS Comput Biol
PMCID: 5501658
PMID: 28640805
DOI: 10.1371/journal.pcbi.1005628

[…] ecificity, accuracy and relatively low MCR. FatHmm_W outperformed FatHmm, both in terms of sensitivity and precision. CADD and FatHmm MCRs were also sensibly low. Among the meta-predictors, CAROL and COVEC WMV, which assembled only two (SIFT and PolyPhen2) and three (SIFT, PolyPhen2 and MutationAssessor) primary scores, respectively, showed decent performances. Pairwise comparisons of predictions […]

call_split

IMHOTEP—a composite score integrating popular tools for predicting the functional consequences of non synonymous sequence variants

2016
Nucleic Acids Res
PMCID: 5388428
PMID: 28180317
DOI: 10.1093/nar/gkw886
call_split See protocol

[…] ernal validation and comparison to other approaches, our top integration methods (random forest, decision tree and logistic regression) and six commonly used integration approaches, namely Condel (), CoVEC (), CAROL (), CADD (with a threshold of 20 for the scaled score) (), MetaSVM and MetaLR (), were also applied to the external validation data.Receiver operating characteristic (ROC) curves were […]

library_books

Computational assessment of feature combinations for pathogenic variant prediction

2016
PMCID: 4947862
PMID: 27468419
DOI: 10.1002/mgg3.214

[…] ness. Recently, individual predictors have been combined into consensus predictors to further improve prediction performance. The most prominent examples are Condel (González‐Pérez and López‐Bigas ), CoVEC (Frousios et al. ), and PredictSNP (Bendl et al. ).An important issue of these consensus predictors is the potential overlap of training and validation data. Performance evaluation on variants t […]

Citations

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CoVEC institution(s)
Department of Informatics, King's College London, Strand Campus, The Strand, London, UK; Institute for Mathematical and Molecular Biomedicine, King's College London, Hodgkin Building, Guy's Campus, London, UK; Department of Medical and Molecular Genetics, King's College London, School of Medicine, 8th Floor Tower Wing, Guy's Hospital, London, UK
CoVEC funding source(s)
Supported by the Greek State Scholarships Foundation; the Department of Health via the National Institute for Health Research comprehensive Biomedical Research Centre award to Guy's & St Thomas' NHS Foundation Trust in partnership with King's College London and King's College Hospital NHS Foundation Trust.

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