VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions

The Human Genome Variation Society (HGVS) variant nomenclature is widely used to describe sequence variants in scientific publications, clinical reports, and databases. However, the HGVS recommendations are complex and this often results in inaccurate variant descriptions being reported. The open‐so...

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Podrobná bibliografia
Vydané v:Human mutation Ročník 39; číslo 1; s. 61 - 68
Hlavní autori: Freeman, Peter J., Hart, Reece K., Gretton, Liam J., Brookes, Anthony J., Dalgleish, Raymond
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States John Wiley & Sons, Inc 01.01.2018
John Wiley and Sons Inc
Predmet:
Chromosome Mapping - methods
Computational Biology - methods
Databases, Genetic
Exons
Gene mapping
Genetic Variation
HGVS variant nomenclature
Humans
Informatics
Introns
Nomenclature
Nucleotide sequence
reference sequences
Reproducibility of Results
Sequence Analysis, DNA - methods
sequence variants
sequence variation
Software
User-Computer Interface
validation
variant call format
Variation
VCF
Web Browser
HGVS variant nomenclature
VCF
reference sequences
variant call format
sequence variation
sequence variants
validation
ISSN:1059-7794, 1098-1004, 1098-1004
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Popis
Shrnutí:The Human Genome Variation Society (HGVS) variant nomenclature is widely used to describe sequence variants in scientific publications, clinical reports, and databases. However, the HGVS recommendations are complex and this often results in inaccurate variant descriptions being reported. The open‐source hgvs Python package (https://github.com/biocommons/hgvs) provides a programmatic interface for parsing, manipulating, formatting, and validating of variants according to the HGVS recommendations, but does not provide a user‐friendly Web interface. We have developed a Web‐based variant validation tool, VariantValidator (https://variantvalidator.org/), which utilizes the hgvs Python package and provides additional functionality to assist users who wish to accurately describe and report sequence‐level variations that are compliant with the HGVS recommendations. VariantValidator was designed to ensure that users are guided through the intricacies of the HGVS nomenclature, for example, if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator has the facility to interconvert genomic variant descriptions in HGVS and Variant Call Format with a degree of accuracy that surpasses most competing solutions. VariantValidator is a user‐friendly software tool designed to validate the syntax and parameters of DNA variant descriptions according to the HGVS Sequence Variant Nomenclature. VariantValidator ensures that users are guided through the intricacies of the HGVS nomenclature, e.g. if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator accurately interconverts between transcript variant descriptions and genomic variant descriptions in HGVS and Variant Call Format (VCF).
Bibliografia:Funding information
Contract Grant Sponsor: Wellcome Trust (097828/Z/11/B).
Communicated by Peter N. Robinson
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Funding information Contract Grant Sponsor: Wellcome Trust (097828/Z/11/B).
ISSN:1059-7794
1098-1004
1098-1004
DOI:10.1002/humu.23348