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skill CX Codex GP ChatGPT official · OpenAI

finngen-phewas-skill — Codex skill: what it does, how to install

This skill fetches compact FinnGen PheWAS results for one variant. It accepts an rsID or GRCh37/GRCh38 coordinates and resolves the query to GRCh38.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill finngen-phewas-skill -a codex
Open on GitHub

What finngen-phewas-skill does

The skill runs scripts/finngen_phewas.py to look up FinnGen PheWAS associations for one variant. Input can use rsid, grch37, grch38, or variant; the value is resolved to a canonical GRCh38 query in chr:pos-ref-alt form. The result exposes the association count, truncation state, queried variant, and any returned regions.

By default, the script produces a concise Markdown summary and starts with max_results=10. Set save_raw=true when the full payload should be written to a file through raw_output_path instead of pasted into chat. Python is required to run the script, and the skill uses scripts/finngen_phewas.py as its lookup entry point. Exactly one variant identifier is allowed per request, so passing several input forms together will fail validation.

What it helps with

  • look up FinnGen associations for one variant
  • resolve GRCh37 coordinates to a GRCh38 query
  • retrieve a compact PheWAS summary by rsID
  • save the full JSON response to a file

Example prompts for the agent

  • Check FinnGen PheWAS for `rs7903146` and give me a concise summary.
  • Look up `10:114758349-C-T` in GRCh37 and report the canonical GRCh38 variant.
  • Fetch results for `10:112998590:C:T`, raise `max_results` to `25`, and save the full response to a file.

How to install finngen-phewas-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill finngen-phewas-skill -a codex

2Manually: put the files in place

.agents/skills/finngen-phewas-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about finngen-phewas-skill

How do I install finngen-phewas-skill in Codex?

Run npx skills add openai/plugins --skill finngen-phewas-skill, then run npx skills add openai/plugins --skill finngen-phewas-skill -a codex. The skill file is available at .agents/skills/finngen-phewas-skill/SKILL.md.

What does finngen-phewas-skill do?

It looks up compact FinnGen PheWAS results for one variant and resolves an rsID or GRCh37/GRCh38 coordinates to a GRCh38 query. The summary includes the association count, truncation state, and returned regions.

What input can the skill accept?

Pass exactly one of rsid, grch37, grch38, or variant. You can also provide max_results, save_raw, raw_output_path, or timeout_sec.

See also

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