Figure 4

Applying a GQ filter improves the quality of imputation results from WES data. Plots illustrate data quality improvement seen after applying GQ threshold. A) Plots the average concordance (blue line) improvement between array and sequencing genotypes for 10 samples as the GQ threshold increases. Coupled with this concordance improvement is the average percent of genotypes that remain (red line) with GQ values above that threshold. B) At the GQ > 20 threshold, this plot shows that variants removed (blue) due to loss of all genotypes have generally lower quality (as measured by R²) compared to variants containing at least one genotype (red). Mean values for each distribution are shown by the dotted lines.