Table 2

Comparison of SVseq2, SVseq1 and Pindel using real individual data.

SVseq2(3)

SVseq2(4)

SVseq1

Pindel

F

SE

SO

F

SE

SO

F

SE

SO

F

SE

SO


NA19311

48

38(79%)

44(92%)

24

24(100%)

24(100%)

15

14(93%)

14(93%)

3

2(67%)

2(67%)

NA19312

47

27(57%)

32(6872%)

19

16(84%)

16(84%)

28

12(43%)

20(72%)

9

2(22%)

7(78%)

NA19313

70

23(33%)

43(61%)

27

16(59%)

22(81%)

70

21(30%)

51(73%)

14

3(21%)

12(85%)

NA19316

17

14(82%)

16(94%)

4

3(75%)

4(100%)

3

2(67%)

3(100%)

7

5(71%)

6(86%)

NA19317

28

18(64%)

22(79%)

13

10(77%)

10(77%)

6

4(67%)

4(67%)

4

2(50%)

4(100%)


SVseq2 is run with cutoff values 3 and 4. The cutoff value is 3 for SVseq1 and Pindel. F stands for "Findings", SE for "Supported by exact breakpoints" and SO for "Supported by overlap". Numbers in the parenthesis are accuracies.

Zhang et al. BMC Bioinformatics 2012 13(Suppl 6):S6   doi:10.1186/1471-2105-13-S6-S6

Open Data