Table 1 Performance increases by restricting variant calling in HCI regions and coding regions.

From: Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA

Oncopanel

Recall (%)

Precision (%)

F1-score (%)

Average

Maximum

Average

Maximum

Average

Maximum

Performance increases by restricting variant calling in HCI regions

 Oncopanel A

2.03 ± 5.81

12.42

11.75 ± 7.14

27.50

5.41 ± 6.57

17.41

 Oncopanel B

3.40 ± 3.61

9.57

3.66 ± 9.27

36.04

1.87 ± 3.64

10.31

 Oncopanel X

7.20 ± 7.59

17.81

2.63 ± 5.89

18.82

2.87 ± 6.13

13.44

Performance increases by restricting variant calling in coding regions

 Oncopanel A

− 0.60 ± 3.34

5.73

9.28 ± 6.01

21.68

3.50 ± 3.72

10.13

 Oncopanel B

− 0.77 ± 2.41

7.07

0.91 ± 4.72

18.22

0.73 ± 2.48

4.72

 Oncopanel X

1.58 ± 5.32

9.29

0.55 ± 5.85

17.81

0.21 ± 5.42

9.19

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