Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-gwasgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gwas)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gwas"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gwas/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gwas"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gwas.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00085 | $0.01611 |
| Opus 5 | $0.00043 | $0.00805 |
| Sonnet 5 | $0.00017 | $0.00322 |
| Haiku 4.5 | $0.00009 | $0.00161 |
Grade A, and why
alterlab-gwas scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) How it starts
The opening of the file, as written. The whole thing — 96 lines — stays where its author put it; the contents beside it link to each section on GitHub.
GWAS Catalog Database
Overview
The GWAS Catalog is a curated repository of published genome-wide association studies maintained by NHGRI and EBI. It contains SNP-trait associations from thousands of GWAS publications — genetic variants, associated traits and diseases, p-values, effect sizes, and full summary statistics for many studies.
Scripts
scripts/query_gwas.py — query the GWAS Catalog REST API (stdlib only, JSON to stdout):
python scripts/query_gwas.py variant rs7903146 # associations for a SNP
python scripts/query_gwas.py trait MONDO_0005148 --size 100 # associations for a trait
python scripts/query_gwas.py study GCST001795 # study metadata
When to Use This Skill
Use this skill for:
- Genetic variant associations — SNPs associated with diseases or traits
- SNP lookups — information about specific variants (rs IDs)
- Trait/disease searches — genetic associations for phenotypes
- Gene associations — variants in or near specific genes
- GWAS summary statistics — complete genome-wide association data
- Study metadata — publication and cohort information
- Population genetics — ancestry-specific associations
- Polygenic risk scores — variants for risk prediction models
- Functional genomics / systematic reviews — variant effects, literature synthesis
Data Model
Four core entities, each with a canonical identifier:
- Studies →
GCSTaccessions (e.g., GCST001234) - Associations → SNP-trait links with p-values (genome-wide significant: p ≤ 5×10⁻⁸)
- Variants →
rsnumbers (e.g., rs7903146) - Traits → trait ontology short-forms (e.g., MONDO_0005148 = type 2 diabetes on the main REST API); genes use HGNC symbols (e.g., TCF7L2)
Trait-ID gotcha (verified): the two APIs disagree on trait IDs. The main REST API has migrated many traits to MONDO / current EFO short-forms, so
efoTraits/MONDO_0005148works but the legacyefoTraits/EFO_0001360now 404s. The Summary Statistics API still uses the legacy ID:traits/EFO_0001360works there buttraits/MONDO_0005148404s. If a trait path 404s, look up the current short-form with/efoTraits/search/findByTrait?trait=...(main API) before assuming the trait is absent.
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 96 lines · 85 tokens per session scan A a58b88e9ff52
alterlab-gwas is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 7d ago), licensed MIT. It adds 85 tokens to every session and 1,611 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-05.
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