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Search and interpret NCBI ClinVar variant data, access via E-utilities or FTP, annotate VCFs, and incorporate review-status and evidence best practices for geno
This skill equips an agent to query and interpret ClinVar — NCBI's archive of variant clinical significance — for research and annotation workflows. It provides search patterns, programmatic E-utilities examples, bulk FTP download instructions, and guidance for parsing XML/VCF/tab-delimited formats to annotate variant call sets and build local databases. The skill stresses review-status (star ratings), conflict resolution strategies, and reproducible versioning.
Use when you need authoritative ClinVar lookups, to annotate VCFs with clinical significance, to bulk-download ClinVar releases for pipeline construction, or to investigate conflicting variant interpretations. Not intended for making clinical decisions without genetics professionals.
Useful for research-focused assistants and bioinformatics-capable models that can run command-line tools and Python for data processing (e.g., Codex, Claude Code-like agents).
ClinVar query skill for bioinformatics — searches NCBI's ClinVar database via E-utilities API for variant clinical significance. SKILL.md is comprehensive with detailed examples, API reference pointers, and important caveats about field tag behavior. The bundled script (query_clinvar.py) is clean and well-structured but requires a subcommand argument (search/summary) and doesn't run standalone without args, hence the argparse exit code 2 under DRY_RUN.
No security concerns. Network calls only to NCBI E-utilities (legitimate public API). API key properly sourced from env var, no hardcoded credentials. Skill is well-documented with thorough examples and important warnings about ClinVar field tags silently falling back to [All Fields].
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