Figure 3.

The effect of Alternate Allele Depth and Alternate Allele Frequency on variant calling agreement across workflows and platforms. For each panel, calls made by all but one workflow (A–D) or both platforms (E–H) were considered true-positives, while calls made by only a single workflow (or technology) were considered false-positives, thus the ROC AUCs cannot be directly compared between groups. For the right panels, points represent an Allele Frequency (AF) cut-off of 1 at the lower-leftmost point, and the cut-off decreases by 0.1 along the length of the line. For the left panels, the points represent a minimum Alternate Allele Depth (AltDP) going from 4,000 at the lower-left most point to 10 along each line. (A,B) Impact of AltDP and AF, respectively, on Illumina workflow accuracy and specificity across workflows. (C,D) Impact of AltDP and AF, respectively, on Illumina workflow accuracy and specificity across platforms. (E,F) Impact of AltDP and AF, respectively, on ONT workflow accuracy and specificity across workflows. (G,H) Impact of AltDP and AF, respectively, on ONT workflow accuracy and specificity across platforms.