Finngen Phewas Skill for Codex

Fetch compact FinnGen PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise FinnGen association results for one variant

6k tokens

context cost

the whole folder, loaded on every use

files

ships runnable scripts

copies elsewhere

how many repositories repackaged it

4915

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/openai/plugins --skill finngen-phewas-skill

What comes with it

19 708 bytes besides the instruction

agents/openai.yaml

scripts/finngen_phewas.py

scripts/variant_resolution.py

The instruction itself

6 sections, as written by the author

Operating rules

Use scripts/finngen_phewas.py for all FinnGen PheWAS lookups.
Accept exactly one of rsid, grch37, grch38, or variant; resolve to the canonical GRCh38 chr:pos-ref-alt query before calling FinnGen.
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, truncation status, and any returned regions.
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:
{"grch38":"10:112998590-C-T","max_results":10}
{"grch37":"10:114758349-C-T","max_results":10}
{"rsid":"rs7903146","max_results":10}
{"variant":"10:112998590:C:T","max_results":25,"save_raw":true}

Output

Success returns ok, source, input, query_variant, max_results_applied, association_count, association_count_total, truncated, associations, variant, regions, variant_url, raw_output_path, and warnings.
Use raw_output_path when save_raw=true.
Failure returns ok=false with error.code and error.message.

Execution

echo '{"grch38":"10:112998590-C-T","max_results":10}' | python scripts/finngen_phewas.py

References

No additional runtime references are required; keep the import package limited to this file and scripts/finngen_phewas.py.

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How to use it

Copy the folder

Take openai/finngen-phewas-skill from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.