gwascatalog.sumstatapp 0.1.0

Data validation applications for GWAS Catalog submissions

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.

[!WARNING] This is a work in progress. The current version of the package is under active development and may undergo significant changes. The API and functionality are not yet stable, and breaking changes are expected.

What kind of data are supported?

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

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.).