Script for generating the PRS scores & Mendelian Randomisation analysis for the collaborative COVID-19 research.
Please note that the variant IDs in the target BED shoud follow CHR(numeric):BP(numeric) [i.e. 19:971949].
If the target BED contains the rsIDs as variant identifier, update the IDs using PLINK 2.00:
plink2 --bfile [target_BED] --snps-only --set-all-var-ids '@:#' --make-bed --out [modified_target_BED]
R version 3.2.3 or higher
PLINK 2.00 or higher
git clone https://github.com/RezaJF/COVID19_PRS.git
cd COVID19_PRS
./PRS_calculation.sh [PATH_to_PRSice] [PATH_to_imputed_BEDs] [OUTPUT_DIRECTORY]- For accessing accompanying summary statistic data, please contact directly!
For more update and instructions email me at: [email protected] or [email protected].