Extracting gene–disease associations from the GWAS Catalog

The GWAS Catalog compiles associations from published GWAS [ref]. We're using the resource in rephetio, our network for drug repurposing. This repository extracts associations for the diseases and genes in rephetio.

Execution

The notebooks are executed as follows:

• windows.ipynb processes the results of a SNAP proxy search to extract windows (genomic regions) around each lead SNP based on linkage disequilibrium (data/snap/windows.tsv). See this discussion for details.

• loci.ipynb extracts disease–loci (SNP) associations (data/snp-associations.tsv) and disease–gene associations (data/gene-associations.tsv).

License

GWAS Catalog downloads and derivatives are licensed under CC BY 4.0 in accordance with the EBI's terms of use. All original content in this repository is licensed under CC0 1.0.