Source: https://github.com/aipoch/medical-research-skills

When to Use

You need to find ClinVar variant records by gene, condition/phenotype, or clinical significance (e.g., BRCA1 + pathogenic).
You want to interpret a variant’s clinical significance (Pathogenic/Benign/VUS) and review status for reporting or triage.
You need to annotate a VCF with ClinVar identifiers and interpretation fields as part of a variant annotation pipeline.
You want to perform bulk retrieval of ClinVar datasets for offline analysis or periodic database refresh.
You are building a workflow that relies on NCBI E-utilities to programmatically query ClinVar.

Key Features

ClinVar search via NCBI E-utilities using flexible query terms (gene/condition/significance).
Clinical interpretation retrieval, including clinical significance categories and review status.
VCF annotation workflow integration (leveraging bcftools) to enrich variants with ClinVar data.
Bulk data access through ClinVar FTP downloads for large-scale processing.
Reference documentation:
- API details: references/api_reference.md
- Clinical significance definitions: references/clinical_significance.md