ols.md

Perform Association Study, i.e. OLS regression

After getting the data, we are now ready to perform the OLS regression.

To use GRE, be sure to perform the association studies with the exactly same genotype you use to compute the LD. We leave GRE with reference panel LD for future work.

num_cols=$(head -1 $covar_file | awk '{print NF}')
num_cols=$((num_cols-2))

for chr_i in $(seq 1 22)
do
plink \
  --allow-no-sex \
  --bfile ${all_bfile} \
  --chr ${chr_i} \
  --ci 0.95 \
  --covar ${covar_file} \
  --covar-number 1-${num_cols} \
  --linear hide-covar \
  --out ./assoc/chr${chr_i} \ 
  --pheno ${pheno_file}
done

You will get 22 association files after this step. Each contains the OLS sumstats for SNPs for 22 chromosomes.