I have handled many genotype datasets from SNP-array dataset or WES dataset. I found the standard PLINk QC methods for GWAS cannot be applied to genotype dataset from WES simply. For example, relatedness check step will screen more outliers. The heterozygous rate scale is smaller. It is kind of hard for me to understand the reason. Many people told me if you have WES or WGS data, no need to have SNP array data. I think there may be some critical difference. Any explanation will be appreciated.