gnomad-graphql-skill

Query the gnomAD GraphQL API for variant frequency and gene constraint summaries.

5.3k|765|Updated Mar 4, 2026
One-click install
npx skills add https://github.com/openai/plugins --skill gnomad-graphql-skill
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: gnomad-graphql-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/gnomad-graphql-skill
Command: npx skills add https://github.com/openai/plugins --skill gnomad-graphql-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

Researchers often need quick, targeted answers from the gnomAD database without writing and debugging raw GraphQL requests or parsing huge JSON payloads. This Skill submits compact gnomAD GraphQL queries and returns concise, readable summaries of variant frequencies, gene constraint metrics, and transcript consequence context.

Core Features & Use Cases

  • Compact GraphQL Execution: Sends queries to the gnomAD API endpoint with variables, timeouts, and truncation controls, returning trimmed summaries instead of overwhelming raw dumps.
  • Flexible Input Options: Accepts inline queries or a query_path file for long GraphQL documents, plus optional max_items, max_depth, and save_raw settings.
  • Structured Error Reporting: Returns clear error codes such as network_error, graphql_error, or invalid_input so failures are easy to diagnose.
  • Use Case: Ask for the allele frequency of variant 1-55516888-G-GA in gnomAD v4 and receive a short markdown summary with ac, an, and af values instead of the full API response.

Quick Start

Ask the assistant to look up the allele frequency of a specific variant in gnomAD r4 and summarize the result.

Frequently Asked Questions about gnomad-graphql-skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query the gnomAD API for variant allele frequencies?

Send a GraphQL query with the variantId and dataset variables, such as gnomad_r4, through the gnomad_graphql.py script. It returns a compact summary containing ac, an, and af fields instead of the full raw response.

How do I run a long GraphQL query against gnomAD?

Save the query to a file and pass its path via the query_path field instead of inlining the query text. This keeps requests manageable and avoids pasting large GraphQL documents into the input JSON.

Can I get the full raw JSON response from gnomAD?

Yes, set save_raw to true in the input JSON and optionally specify raw_output_path. The script writes the complete response to disk and reports the saved file path alongside the compact summary.

Why does my gnomAD GraphQL request return a graphql_error?

A graphql_error means the gnomAD server rejected the query, usually due to invalid field names, wrong dataset identifiers, or malformed syntax. Check the error message returned in the response and verify the query against the gnomAD schema.

What Python dependencies does the gnomAD GraphQL script need?

The script requires only the requests library to POST queries to the gnomAD API endpoint. If requests is missing, it returns a missing_dependency error explaining the import failure.