Fig. 3

Precision vs Recall of NS12911 based ∼30× fold coverage simulated reads is shown for Indels (top) and SNPs (bottom). Solid lines represent EAGLE’s likelihood. Dotted lines represent the caller’s quality score. Recall levels are shown in increments of 50 variant calls with the maximum level based on the number of variants in the NS12911 benchmark set. The variant calls were ranked based on our model’s marginal posterior probability or each caller’s quality score respectively. Precision is the fraction of high ranking variants which are correct, plotted over a wide range of thresholds