MOVE on UK Biobank

This repository aggregates SNPs across the high-quality GWAS results of the Pan-UK Biobank project. Using a threshold of -log10(p-value) > 16, and using all high-quality GWAS the aggregated file with -log10 pvalues contains X SNPs from Y studies.

Setup

Using anaconda for environments

conda create -n ukbio python pip pandas ipykernel
conda install -c conda-forge -c bioconda snakemake

Single GWAS results

The high-quality GWAS can be downloaded using the Snakemake workflow. An overview of the single GWAS results of the Pan-UK Biobank project can be found here

I provided a brief script which creates a config/high_quality_gwas.yaml file for the Snakemake workflow in 0_get_high_quality_gwas.py.

Snakemake

The Snakemake workflow can be executed using the following command with one job at a time:

snakemake -c1 -n # dry-run
snakemake -c1 # run

Slurm cluster script

The slurm script can be used to run the Snakemake workflow on a slurm cluster: bin/slurm_execute.sh.