This pre-processing procedure requires:

• QCTOOL, version 1.0
• GTOOL, version 1.0
• PLINK, version 2.00
• Python, version 3.7.4

Before starting the pre-processing procedure, the script paths_and_parameters.sh should be modified to add information about :

• paths:
  • main project directory: prj_dir
  • QCTOOL software: oxford_dir
  • GTOOL software: oxford_dir2
  • PLINK software: plink_dir
  • genotype data: geno_dir
  • imputed data: imp_dir
  • output data: out_dir
• parameters:
  • list of chromosomes: CHR_LIST
  • SNP call rate: SNP_CALLRATE
  • SNP minor allele frequency: SNP_MAF
  • sample call rate: SAMPLE_CALLRATE
  • window size for linkage disequilibrium analysis: LD_WINDOWSIZE
  • step size for linkage disequilibrium analysis: LD_STEPSIZE
  • coefficient of correlation squared for linkage disequilibrium analysis: LD_R2
  • threshold for Hardy-Weinberg equilibrium analysis: HWE

Pre-processing can be performed by running the script main_script as follows :

bash ./code/main_script.sh

It will successively call the scripts for the different steps, which can be found under ./code/steps_code. Below is a description of each step:

Output examples for each steps can be found under ./code/README.md

• UK Biobank
• PLINK

This repository is maintained by:

• Lucie Bourguignon
• Caroline Weis
• Catherine Jutzeler

Data acquisition and analyses in the present study were conducted under UK Biobank Application #14762.