VariantValidator

VariantValidator validates and converts DNA sequence variant descriptions to ensure compliance with Human Genome Variation Society (HGVS) Sequence Variant Nomenclature for research, clinical reporting, and database use.

Key Features:

• HGVS validation: Validates variant descriptions against HGVS Sequence Variant Nomenclature recommendations.
• Error detection and correction: Automatically detects errors in variant descriptions and attempts correction when possible.
• Interconversion with VCF: Converts between transcript-level and genomic-level variant descriptions and supports Variant Call Format (VCF) representations.
• Integration with hgvs Python package: Uses the hgvs Python package to parse, format, manipulate, and validate biological sequence variants programmatically.

Scientific Applications:

• Genomic research: Standardizes variant descriptions for reporting in research publications.
• Clinical genomics: Ensures HGVS-compliant variant descriptions in clinical reports and patient data management.
• Database management: Improves consistency and quality of variant entries in genomic databases.

Methodology:

Parses, formats, manipulates, and validates HGVS variant descriptions using the hgvs Python package; performs interconversion between transcript and genomic descriptions and VCF; detects and attempts to correct errors according to HGVS recommendations.