Summary of methods and improved data quality from genotype and variant filters. A) Left panel illustrates the standard filtering method (left side) compared to the proposed genotype and variant filtering method (right side) for sequencing data. Right panel illustrates the method used for genotype and variant filtering of imputed data. The quality metrics resulting from standard filtering (blue box), proposed genotype and variant filters (orange boxes), and a combination of these methods (green box) are compared to the quality of the unfiltered data (grey boxes). B) Quantitative comparisons of quality improvement are depicted for both sequencing and imputation filters at both genotype (% of discordant genotypes removed and % concordance) and variant (Ti/Tv and R2) levels. Box colors match the boxes in A).