Figure 2

Improved concordance, sensitivity and specificity of WES data using genotype filters. Plots illustrate the non-reference concordance and sensitivity versus specificity between array and sequencing genotypes for 10 samples. A) The percent of non-reference discordant calls removed is plotted versus the percent of non-reference concordant calls retained at increasing quality thresholds. B) Sensitivity versus specificity is plotted at increasing quality thresholds. For A) and B), blue line represents changing DP thresholds and the red line represents change GQ thresholds. Chosen filter thresholds (DP ≥ 8 and GQ ≥ 20) are indicated by points on these lines. C) Summarizes the effect that the chosen genotype filters (both DP and GQ) have on non-reference concordant and discordant genotype calls with and without the VQSR filter.