from alterlab-academic-skills18
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).
This skill has not been reviewed by our automated audit pipeline yet.
