The quality of single nucleotide polymorphisms (SNPs) is of paramount importance for genome-wide association studies (GWAS) to reduce potential false findings. The SNP genotyping data are not always accurate because of various reasons such as experimental systematic errors. SNP quality control methods commonly use filter-by-extreme filters based on quality control variables of Hardy-Weinberg equilibrium (HWE), missing frequency (MiF) and minor allele frequency (MAF), to remove outliers. These filters neglect the fact that variables may contribute differently for different SNP clusters, and the...
