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Table 2 Quality evaluation of variant detection using different variant-calling pipelines.

From: Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

 

Sensitivity

 

Specificity

 

Mean*

SD

Mean*

SD

SOAPsnp

94.68

2.26

99.79

0.03

GATK1.5

95.34

1.16

99.72

0.08

SNVer

92.33

4.40

99.78

0.04

GNUMAP

86.60

3.23

99.64

0.06

SAMtools

94.47

4.22

99.59

0.16

Any pipeline

97.67

1.20

99.62

0.11

≥ 2 pipelines*

96.64

2.28

99.69

0.07

≥ 3 pipelines*

95.62

3.13

99.73

0.05

≥ 4 pipelines*

92.60

3.40

99.82

0.04

5 pipelines*

80.58

5.26

99.87

0.01

  1. *Intersection of variants contained in the number of pipelines specified.
  2. Sensitivity and specificity was calculated for each pipeline by comparing Illumina Human610-Quad version 1 SNP arrays with exome-capture sequencing results, based on the four samples whose genotyping data was available.
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Genome Medicine

ISSN: 1756-994X

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