clingen-cyvcf2-variants

What problem does it solve?

This Skill enables researchers to automatically build a curated database of pathogenic cardiac variants by parsing VCF data, extracting coordinates and dbSNP rsIDs, and annotating molecular consequences for downstream analysis.

Core Features & Use Cases

• VCF parsing with cyvcf2 to extract CHROM:POS:REF:ALT coordinates, gene, and rsID.
• Validation of VCF coordinates and rsID formats with strict ACMG-relevant criteria.
• Generates a YAML variant catalog with fields: gene, chrom_pos_ref_alt, rsid, clinical_significance, condition, molecular_consequence, population_frequency.
• Use Case: create a lethal_variant_db.yaml for automated pathogenic variant curation in clinical genomics workflows.

Quick Start

Run the clingen-cyvcf2-variants workflow on a VCF with cyvcf2 to populate a lethal_variant_db.yaml.