Column and format standardisation
Detect common GWAS summary-statistics fields and map uploaded files into a consistent structure for comparison, meta-analysis preparation, genetic correlation, and downstream bioinformatics.
GWAS summary-statistics alignment
GWAS Harmoniser
GWAS Harmoniser is a web tool for aligning alleles, standardising columns, handling genome builds and rsIDs, previewing quality-control plots, and exporting harmonised GWAS summary statistics.
Use GWAS Harmoniser to align GWAS sumstats for cross-study comparison, meta-analysis preparation, genetic correlation, and downstream bioinformatics workflows.
Align and harmonise GWAS summary statistics
Allele alignment
Check reference, alternate, effect, and non-effect alleles and prepare variants for consistent interpretation across datasets.
Genome-build and variant handling
Support build-aware workflows, coordinate liftover, and rsID validation or addition when preparing GWAS summary statistics.
Quality-control preview and export
Inspect row previews, alignment logs, Manhattan plots, and QQ plots before preparing harmonised outputs for download.
GWAS summary-statistics harmonisation FAQ
How can I align GWAS summary statistics?
Upload a GWAS summary-statistics file, confirm the detected columns and genome build, select the required allele, build, and rsID options, inspect the harmonisation preview, and export the aligned result.
What does GWAS Harmoniser align?
GWAS Harmoniser standardises common summary-statistics columns and supports reference, alternate, effect, and non-effect allele handling, build-aware coordinate workflows, rsID checks, and consistent export preparation.
Can GWAS Harmoniser prepare sumstats for meta-analysis?
GWAS Harmoniser can standardise fields and help align alleles, coordinates, and identifiers before cross-study comparison or meta-analysis. Researchers must still verify cohort metadata, analysis models, genome-build provenance, and study-specific quality-control requirements.
Does GWAS Harmoniser support genome-build liftover?
GWAS Harmoniser supports build-aware processing and liftover workflows so coordinates can be prepared consistently when source and target reference assemblies differ.
Does GWAS Harmoniser support large GWAS files?
The application is designed around reliable uploads, preview generation, background download preparation, and polling for large GWAS summary-statistics files.
Who should use GWAS Harmoniser?
GWAS Harmoniser is intended for researchers, geneticists, statistical geneticists, epidemiologists, and bioinformaticians preparing GWAS summary statistics for downstream analysis.
Harmonize GWAS sumstats with an AI agent
Use Codex or Claude Code to harmonise GWAS summary statistics through MCP. Standardise columns, align alleles, convert genome builds and validate rsIDs, with QC records for the run.
Codex and Claude Code can use the bundled Agent Skill and MCP server. See the agent and MCP guide for installation, routing examples, data handling and scientific checks.
Scientific scope and limitations
GWAS Harmoniser supports data harmonisation and preparation, but it does not replace validation of cohort metadata, genome-build provenance, allele conventions, quality control, or downstream statistical analysis.