ClinVar Genomic Analysis

About

This skill integrates the NCBI ClinVar database into the Claude Code environment, allowing researchers and bioinformaticians to programmatically search for human genetic variants, interpret clinical significance, and process bulk genomic data. It provides standardized guidance for navigating the E-utilities API, interpreting ACMG/AMP pathogenicity classifications, and automating VCF annotation. By bridging the gap between raw genomic files and clinical evidence, it streamlines the analysis of variant-phenotype relationships and supports evidence-based genomic medicine workflows.

Key Features

• Programmatic ClinVar querying via NCBI E-utilities API
• VCF annotation and filtering for clinical significance using tools like bcftools
• High-confidence variant filtering based on star-rating review status
• Automated interpretation of ACMG/AMP pathogenicity classifications
• 2,188 GitHub stars
• Bulk genomic data processing and FTP site navigation

Use Cases

• Identifying pathogenic variants for specific genes in clinical research pipelines
• Building local genomic databases by parsing large-scale ClinVar XML releases
• Resolving conflicting variant interpretations using evidence-based heuristics