ukb-topmed-phewas-skill

Operating rules

• Use scripts/ukb_topmed_phewas.py for all UKB-TOPMed PheWAS lookups.
• Accept exactly one of rsid, grch37, grch38, or variant; resolve to the canonical GRCh38 chr:pos-ref-alt query before calling UKB-TOPMed.
• The script accepts max_results; start with max_results=10 and only increase it if the first slice is insufficient.
• Re-run the lookup in long conversations instead of relying on older tool output.
• Treat displayed ... in tool previews as UI truncation, not literal request content.
• If the user needs the full association payload, set save_raw=true and report raw_output_path instead of pasting large arrays into chat.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return the JSON verbatim only if the user explicitly asks for machine-readable output.
• Surface the canonical queried variant, total association count, and whether the results were truncated.
• Increase max_results gradually instead of asking for large association dumps in one call.

Input

• Read one JSON object from stdin, or a single JSON string containing the variant.
• Required input: exactly one of rsid, grch37, grch38, or variant
• Optional fields: max_results, save_raw, raw_output_path, timeout_sec
• Common patterns: