domains / families / research / clinvar-database

clinvar-database

combined

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine. Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.

When to use

• Searching for variants by gene, condition, or clinical significance
• Interpreting clinical significance classifications (pathogenic, benign, VUS)
• Accessing ClinVar data programmatically via E-utilities API
• Downloading and processing bulk data from FTP
• Understanding review status and star ratings
• Resolving conflicting variant interpretations
• Annotating variant call sets with clinical significance
• You need to find ClinVar variant records by **gene**, **condition/phenotype**, or **clinical significance** (e.g., *BRCA1* + *pathogenic*).

Skill page

Conflict

Both skills cover querying ClinVar, interpreting significance, and bulk data access, but they diverge significantly in implementation details and scope. The first skill (aipoch) is a wrapper around specific Python scripts (`scripts/search.py`, `scripts/annotate.py`) and relies on `bcftools` for annotation. The second skill (FreedomIntelligence) provides direct API usage examples (curl), detailed FTP file paths, specific update schedules, and manual `bcftools` commands for filtering/annotation without relying on the first skill's custom scripts. Combining them is necessary to capture both the script-based workflow and the direct API/FTP procedural details.