Individual SNPs are removed for any of the following reasons: Imprecise mapping to the genome (some SNPs map to multiple places)Excessive disagreement among duplicated samplesExcessive missing genotypes on subjects (e.g., > 5%)Low minor allele frequency (e.g., < 1%)Observed genotype frequencies deviate markedly from expectations (e.g., Hardy-Weinberg equilibrium p < 1 × 10−6)
