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Table 3 Comparison of four approaches on indels using simulated WES data

From: 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

indels

2-kupl

DiscoSNP++

Lancet

GATK-MuTect2

True positive

42

29

40

49

False positive

16

1

44

26

False negative

39

52

41

32

Recall

0.52

0.36

0.49

0.60

FDR

0.27

0.03

0.52

0.35

Precision

0.72

0.97

0.47

0.65

F1 score

0.60

0.52

0.48

0.63