ClinVar Database Integration

概要

This skill provides a specialized interface for interacting with NCBI's ClinVar database, the primary archive for human genetic variation and its relationship to health. It enables researchers and developers to programmatically search variants via E-utilities API, process bulk datasets from FTP servers, and annotate VCF files with clinical pathogenicity classifications. By automating the interpretation of ACMG/AMP guidelines and star-rated evidence levels, it streamlines genomic medicine workflows and helps resolve conflicting variant interpretations within bioinformatics pipelines.

主な機能

• Automated interpretation of pathogenicity classifications and star-rated review status
• Heuristics for resolving conflicting variant interpretations and tracking classification updates
• VCF file annotation and filtering integration with bcftools and Python
• 1 GitHub stars
• Programmatic access to NCBI E-utilities API for searching and fetching records
• Bulk data processing from FTP in XML, VCF, and tab-delimited formats

ユースケース

• Automating the retrieval of pathogenic variants for specific genes like BRCA1 or CFTR
• Annotating genomic variant call sets (VCF) with clinical significance data for diagnostic research
• Building and maintaining local bioinformatics databases by parsing monthly ClinVar XML releases