Copyright holder: EMBL-European Bioinformatics Institute (Apache 2 License)
This script is designed to automatically finemap and highlight the causal variants behind GWAS results by cross-examining GWAS, population genetic, epigenetic and cis-regulatory datasets.
Its original design was based on STOPGAP.
Type '''make download''' to download public databases. Type '''make process_databases''' to preprocess the databases. Type ''' make process_1000G to preprocess 1000Genomes data from the raw vcf.gz files. This can take a long time, it is recommended to download the processed files directly.
By default, run from the root directory the command:
'''
python scripts/gwas_to_genes.py --disease autism
'''
Multiple disease names can be provided.