GWAS Pleiotropic Tool
PRIMe: a Pleiotropic Region Identification Method
The PRIMe source code and files needed to analyze the GWAS Catalog Chromosome 12 data can be downloaded here.
After unzipping, please run the PRIMe.plot.sh command file.
The PDF plots will be generated in the "output" folder.
Below are the options used in the command.
-p 0.00001 => assocation p-value threshold for SNPs to be included
-l 0.8 => LD threshold for SNP pairs to be considered as driver/passenger
-e 4 => the Pleiotropy Index threshold for plots to be generated
-i => input data
-o => output directory
-c => chromosome number