Overall, the relative proportion of SV classes that pass genotype filtering thresholds followed a similar pattern to those that passed SV call quality thresholds with the most SVs being retained on the largest chromosomes. While the size distribution of SVs was somewhat similar to those filtered for call quality (Supplemental Figure 2 and Supplemental Table 2), the proportion of individual chromosomes impacted was no longer consistent among tools and did not follow a clear pattern (Supplemental Figure 3). Of the genotyped filtered datasets tested for Mendelian Inheritance, Sniffles had the highest proportion of genotypes pass all parent-offspring trios tested for Mendelian Inheritance while the Delly dataset had the lowest proportion of SV pass at this threshold (Table 3). As the stringency of the Mendelian Inheritance tests were relaxed, the proportion of passing SVs increased for all datasets (Table 3).