GWAS Catalog: Beyond SNPs

This Python monorepo contains packages and documentation designed to help users prepare non-SNP GWAS summary statistics for submission to the GWAS Catalog.

What kind of data are supported?

Type of genetic variant	Supported
Single nucleotide polymorphism (SNP)	❌, see gwas-sumstats-tools
Copy number variant (CNV)	✅
Gene	✅

Using the validation CLI for bulk data processing

Tip

If you prefer not to work in a terminal or you find it difficult to use please try the web app

First, install uv, then run:

$ uvx --from gwascatalog-sumstatapp gwascatalog beyondsnp validate --help

You should see:

Validate GWAS summary statistics files for submission to the GWAS Catalog.

positional arguments:
  INPUT                 Files to validate

options:
  -h, --help            show this help message and exit
  --type {CNV,GENE}     Type of genetic variation (CNV or GENE)
  --assembly {GRCh38,GRCh37,NCBI36,NCBI35,NCBI34}
                        Genome assembly (e.g. GRCh38)
  --effect-size {beta,odds_ratio,hazard_ratio,z_score}
                        Primary effect size measure
  --allow-zero-pvalues  Accept zero as a valid p-value
  -o, --output-dir OUTPUT_DIR
                        Output directory for results (default: ./validated/)

The package is also available from PyPI. You should always install the pydantic extra:

$ pipx install "gwascatalog.sumstatapp[pydantic]"

Documentation

See our docs here. Please create an issue or email gwas-info@ebi.ac.uk if you have any questions or comments. We appreciate community feedback.

Developer notes

This repository is a uv workspace containing two Python packages:

• sumstatlib: Pydantic models and validation public interfaces
• sumstatapp: data validation applications which uses sumstatlib internally, containing two deployment approaches:
  • A Pyodide web application, responsible for browser-based data validation
  • A standard CLI for bulk data processing and eventual integration with the GWAS Catalog backend

User facing website

• The docs directory contains a docusaurus website
• This is the landing page for non-SNP GWAS Catalog submissions, and the compiled static site will be deployed to https://ebi.ac.uk/gwas/apps/beyond-snps
• A custom docusaurus build process is responsible for building the sumstatlib wheel and bundling the sumstatapp web directory as static content

Building the beyond SNPs static site

Development build (assumes deployed to / on localhost:8000):

$ cd docs
$ npm run build:dev
$ npm run serve 

Production build (assumes deployed to a base URL: gwas/apps/beyond-snps)

$ cd docs
$ npm run build

Deploying the static site is pretty simple: just put the compiled assets somewhere (a bucket, a docker image, etc.).