and maximizing genotyping efficiency is attained. Figure 6 shows the proportion of samples (red and blue lines) or SNPs (green line) remaining at different call rate thresholds. Genotyping efficiency can be checked using the --missing option in PLINK. This will produce a file showing genotype missingness rate (1-efficiency) for each individual (proportion of SNPs which failed on each sample), and for each SNP (proportion of individuals for which no genotype was called). Samples below a desired threshold can be eliminated from any downstream analyses by using the --mind option in PLINK. Genotyping efficiency is also an important marker QC step, and is discussed below.
