MAGIC T2D related trait GWAS enrichment analyses in various genomic annotations

There are directories for the GREGOR, fGWAS and GARFIELD analyses. The workflows were run using snakemake version 5.5.0. Ecample configs for a SLURM cluster execution are provided. The analysis directories follow this general pattern:

├── run.sh : for workflow execution
├── Snakefile : Snakemake files(s)	
├── configs
│   ├── cluster.yaml : Cluster job specifications (SLURM)
│   └── config.yaml : Workflow configuration (created from mkconfig.py while using environment variables)
└── scripts : Scripts for analyses
    ├── script1.py
    └── script2.R

Edit the config.yaml providing paths to input files and your email. Given the correct environment variables are set and input data are specificed, example commands in the run.sh files can be use to execute analysis or print a dry run. Most software required can be set up by a conda environment. Conda can be obtained through the Anaconda/Miniconda Python3 distribution.

1. Set up conda and software:

Please install GREGOR, fGWAS and GARFIELD required to compute GWAS enrichment in regulatory annotations. Edit the path to the installed programs in the config.yaml

Analyses

Dry run of <analysis_name>

./run.sh -n

Run analyses by submitting jobs

./run.sh