Skip to main content

Table 1 Effect of local realignment in INDEL calling

From: Impact of post-alignment processing in variant discovery from whole exome data

Metrics

Change (%)

Cases

No.

%

Sensitivity

−5.1 – −4

2

0.71

Sensitivity

−4 – −3

5

1.79

Sensitivity

−3 – −2

5

1.79

Sensitivity

−2 – −1

17

6.07

Sensitivity

−1 – −0.2

34

12.14

Sensitivity

−0.2–0.2

129

46.07

Sensitivity

0.2–1

53

18.93

Sensitivity

1–2

19

6.79

Sensitivity

2–3

12

4.29

Sensitivity

3–4

4

1.43

Precision rate

−0.2–0

33

11.79

Precision rate

0–0.2

219

78.21

Precision rate

0.2–0.4

12

4.29

Precision rate

0.4–0.6

8

2.86

Precision rate

0.6–0.8

5

1.79

Precision rate

0.8–1

3

1.07

  1. Alignments were subjected to duplicate marking and then to local realignment. A total of 280 cases were evaluated, which represent combinations among five mappers, five callers, six divergence levels and two coverage depths (5 and 40x), excluding 20 cases with BWA mapping at 5–10 %. In each case, the change of INDEL calling sensitivity is calculated as the sensitivity after local realignment using 90 % simulated INDELs, subtracted by that after duplicate marking. The change in precision rate is calculated in the same way
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us