COVID19 MR project

Script for generating the PRS scores & Mendelian Randomisation analysis for the collaborative COVID-19 research.

NOTE

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]

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Prerequisite

PRSice-2

R version 3.2.3 or higher

PLINK 2.00 or higher

Basic usage

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!

Contact

For more update and instructions email me at: reza.jabal@einsteinmed.org or mjaf1d14@soton.ac.uk.