Figure 7

Detection performance in the NA12878 individual when restricting false discovery rates. We compared the performance of each tool in terms of sensitivity and novel variant discovery ability when considering only the subset of calls that meet a maximum FDR threshold. Using the results given in Figure 6, each tool’s FDR was calculated for each of the minimum-evidence settings used to generate the respective receiver operating characteristic (ROC) curves. This provided a mapping from the maximum FDR to the subset of calls that meet the associated minimum-evidence threshold for each tool. Sensitivity and FDR were estimated using the 4,095 deletions that were predicted by at least one tool and validated by PacBio or Moleculo alignments. (A) Sensitivity given a maximum FDR threshold. At 5X coverage, an FDR threshold of approximately 10% is achieved with a minimum of four alignments for LUMPY (8.1% FDR), four for GASVPro (10.1% FDR), six for DELLY (11.3% FDR), and nine for Pindel (6.3% FDR). An approximately 20% FDR at 50X coverage requires 8 alignments for LUMPY (18% FDR), 16 for GASVPro (19% FDR), 12 for DELLY (17.6% FDR), and 20 for Pindel (18.8% FDR). LUMPY had the highest sensitivity at both coverage levels and the relative improvement was most substantial at lower coverage. (B) Venn diagrams reflecting the absolute number of variants discovered uniquely and jointly among the different tools at both 10% FDR for 5X and 20% FDR for 50X. In both cases LUMPY found the most number of unique variants. The difference was most dramatic in the 5X coverage experiment, where only 46 out of 665 (6.9%) of the variants found among all four tools were missed by LUMPY. pe, paired-end; rd, read-depth; sr, split-read.