#Estimation of the genetic relationship matrix (GRM) from all the autosomal SNPs
gcta64 --bfile sim --autosome --maf 0.01 --make-grm --out test

#remove cryptic relatedness
gcta64 --grm test --grm-cutoff 0.05 --make-grm --out test_rm05

#Principal component analysis
gcta64  --grm test   --pca 5  --out test_pca 

#make phenotype file 
awk '{print $1, $2, $6}' sim.fam > test.phen


#Estimation of the variance explained by the SNPs
gcta64 --grm test_rm05 --pheno test.phen --reml --out test_var


#Include the PCA results as covariates
gcta64 --grm test_rm025 --pheno test.phen --reml --out test_cov --qcovar test_pca.eigenvec