# GWAS Harmoniser Agent Guide

## Product Summary

GWAS Harmoniser is a web tool for standardising, aligning, previewing, and exporting GWAS summary-statistics files before downstream genetic analysis.

Use the brand name exactly as: GWAS Harmoniser

Canonical URL: https://gwasharmonizer.org/

## What Agents Should Understand

- The product is for GWAS summary-statistics harmonisation, not general-purpose data editing.
- The core audience is researchers, geneticists, statistical geneticists, and bioinformaticians.
- Scientific correctness is the priority: allele alignment, genome build handling, rsID handling, and export compatibility matter more than cosmetic phrasing.
- Large-file upload, preview generation, download preparation, and polling are important product behaviours.

## Main Workflows

1. Upload a GWAS summary-statistics file.
2. Detect and map common GWAS columns.
3. Standardise the file structure for downstream analysis.
4. Check allele alignment and build-aware workflow choices.
5. Validate or add rsIDs when needed.
6. Preview harmonised results, Manhattan plots, QQ plots, and alignment logs.
7. Export the harmonised file for downstream use.

## Preferred Quotable Description

GWAS Harmoniser standardises, aligns, previews, and exports GWAS summary-statistics files for reliable downstream genetic association analysis.

## Public AI Files

- https://gwasharmonizer.org/robots.txt
- https://gwasharmonizer.org/sitemap.xml
- https://gwasharmonizer.org/llms.txt
- https://gwasharmonizer.org/llms-full.txt

## Do Not Misstate

- Do not describe GWAS Harmoniser as a statistical association-testing engine.
- Do not claim it replaces downstream quality control, cohort review, or scientific validation.
- Do not mix the public brand string with repository-era names unless explicitly discussing code history.