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Table 3 Simulated dataset 1 results (100 bp reads)

From: Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data

  40X 30X 20X 10X 4X
Method SE SP ABE SE SP ABE SE SP ABE SE SP ABE SE SP ABE
B-phon 12/12 12/12 0.96 12/12 12/12 1.0 12/12 12/12 0.96 11/12 11/11 1.36 5/12 5/5 0.5
SVD 11/12 11/11 2.7-417 11/12 11/11 4.8-405 11/12 11/11 7.4-389 11/12 11/11 14.7-370 8/12 8/9 29-336
BD 12/12 16/16 185.3 12/12 16/16 189.1 11/12 14/14 171.3 10/12 15/15 137.6 4/12 4/4 153
GASV 12/12 12/12 100-226 12/12 12/12 103-245 12/12 12/12 106-257 12/12 12/12 114-270 10/12 10/10 129-315
CREST 12/12 25/25 1.2 12/12 23/23 1.2 11/12 15/15 0.9 9/12 11/11 0.8 5/12 5/5 1.1
  1. Sensitivity, specificity, and breakpoint error of interchromosomal breakpoint calls across all five coverage levels for all five programs. SE = sensitivity (true events captured/ # true events), SP = specificity (# predictions that capture true events/ # predictions), ABE = average breakpoint error. Since SVDetect and GASV predict a range of breakpoints, we reported their average breakpoint errors as ranges. BreakDancer and CREST tended to have redundant predictions, but we did not count this against specificity since redundant predictions typically supported a single common event. These redundancies could easily be merged into a single prediction. The CREST package includes a program to remove redundancies, but BreakDancer does not address these redundant predictions.