Other SNP-specific analyses are often carried out to remove low quality or unreliable data. For example, some groups remove SNPs with a minor allele frequency (MAF) below a fixed threshold or not in Hardy Weinberg Equilibrium before conducting the statistical analysis. Although SNPs with low MAF can inflate the false positive rate (see Discussion below), departure from Hardy Weinberg Equilibrium in cases may actually be consistent with significant associations [46] and these SNPs should be flagged for further inspection but analyzed nevertheless.
