Consensus Rules in Variant Detection from Next-Generation Sequencing Data
Figure 2
Distribution of accuracy versus recall by different combinations of quality score (QUAL) and read depth (DP) values in two sets (tiers 1 and 2) of SNVs and indels.
(a) Tier One SNVs. (b) Tier Two SNVs. (c) Tier One Indels. (d) Tier Two Indels. For each variant set (panel), each node represents a combination of cutoff values for QUAL and DP. Specifically, the QUAL cutoff was selected by an integer value in the range of 15 to 35 with an increment of 1 each time, and the DP cutoff by an integer value in the range of 3 to 15 with an increment of 1 each time. Then, we evaluated the accuracy, recall, and F score (see text) for each cutoff combination. Note that many nodes are overlapped on the panel and shown by jitter (i.e., points at the same locations are slightly shifted for visibility). The combination of values that could generate the highest F score was selected (shown in red points).