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

Peter J Freeman1, Reece K Hart2,3, Liam J Gretton4

  • 1Department of Genetics, University of Leicester, Leicester, United Kingdom.

Human Mutation
|October 3, 2017
PubMed
Summary
This summary is machine-generated.

The Human Genome Variation Society (HGVS) nomenclature can be complex, leading to errors. VariantValidator is a new web tool that uses the hgvs Python package to help users accurately describe and report genetic variations.

Keywords:
HGVS variant nomenclatureVCFreference sequencessequence variantssequence variationvalidationvariant call format

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The Human Genome Variation Society (HGVS) nomenclature is essential for standardizing the description of genetic variations.
  • Complexity of HGVS recommendations often leads to inaccurate variant reporting in scientific literature and clinical settings.
  • Existing tools lack a user-friendly interface for HGVS variant validation and manipulation.

Purpose of the Study:

  • To develop a web-based tool, VariantValidator, for accurate HGVS variant description and reporting.
  • To provide a user-friendly interface that guides users through HGVS nomenclature complexities.
  • To enable accurate interconversion between HGVS and Variant Call Format (VCF) descriptions.

Main Methods:

  • Utilized the open-source hgvs Python package for core variant parsing and validation functionalities.
  • Developed a web interface to provide programmatic access to HGVS variant validation.
  • Implemented features for automatic error correction and user guidance for HGVS compliance.
  • Integrated functionality for interconverting genomic variants between HGVS and VCF formats.

Main Results:

  • VariantValidator successfully validates and formats HGVS variant descriptions.
  • The tool offers automated correction of common HGVS nomenclature errors.
  • It provides clear guidance to users encountering difficulties with HGVS compliance.
  • Achieved high accuracy in interconverting HGVS and VCF variant representations, outperforming existing solutions.

Conclusions:

  • VariantValidator simplifies the accurate reporting of genetic variations according to HGVS standards.
  • The tool enhances data consistency and reduces errors in genomic variation descriptions.
  • It serves as a valuable resource for researchers, clinicians, and bioinformaticians working with genomic data.