Table 3

Simulated dataset 1 results (100 bp reads)

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


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.

Hayes and Li BMC Bioinformatics 2013 14(Suppl 5):S6   doi:10.1186/1471-2105-14-S5-S6

Open Data