## load PLINK binary data and convert into text format
plink --bfile ExomeChr22 --recode --out ExomeChr22


## calculate missingness in the data
plink --bfile ExomeChr22 --missing --out missing_rate


## calculate MAFs
plink --bfile ExomeChr22 --mind 0.05 --freq --out MAF


## test HW Equilibrium
plink --bfile ExomeChr22 --hardy --mind 0.05 --out HWE


## check relatedness in samples
plink --bfile ExomeChr22 --mind 0.05 --geno 0.05 --maf 0.01 --hwe 0.00001 --genome --out ExomeChr22_IBS


## calculate PCs to control for admixture/stratification
plink --bfile ExomeChr22 --read-genome ExomeChr22_IBS.genome --cluster --mds-plot 10 --out ExomeChr22_stratification


## create clean dataset for association analysis
plink --bfile ExomeChr22 --remove remove_individuals.txt --mind 0.05 --geno 0.05 --maf 0.0025 --hwe 0.00001 --recode --out ExomeChr22_clean