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

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journal contribution
posted on 27.11.2017, 14:40 by Peter J. Freeman, Reece K. Hart, Liam J. Gretton, Anthony J. Brookes, Raymond Dalgleish
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, 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 has the facility to interconvert genomic variant descriptions in HGVS and Variant Call Format (VCF) with a degree of accuracy which surpasses most competing solutions.

Funding

Wellcome Trust. Grant Number: 097828/Z/11/B

History

Citation

Human Mutation, 2017, 1–8.

Author affiliation

/Organisation/COLLEGE OF LIFE SCIENCES/MBSP Non-Medical Departments/Department of Genetics

Version

VoR (Version of Record)

Published in

Human Mutation

Publisher

Wiley for Human Genome Variation Society

issn

1059-7794

eissn

1098-1004

Acceptance date

25/09/2017

Copyright date

2017

Available date

27/11/2017

Publisher version

http://onlinelibrary.wiley.com/doi/10.1002/humu.23348/abstract

Language

en