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Table 1 Intersection of calls obtained using different alignment pipelines

From: Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

  

TP - 100% NA12878a

FP

BWA/GATK only (%)

Intersection

Novocraft only (%)

BWA/GATK only (%)

Intersection

Novocraft only (%)

SNVs

Mutect2

90 (1.1)

8435

91 (1.1)

23 (65.7)

12

15 (55.6)

Strelka

107 (1.3)

7928

37 (0.5)

12 (50.0)

12

5 (29.4)

Indels

Mutect2

11 (6.4)

162

6 (3.6)

3 (60.0)

2

2 (50.0)

Strelka

7 (4.0)

169

3 (1.7)

0 (0.0)

2

8 (80.0)

  1. aOut of 9968 candidate SNVs and 420 true positive
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Genome Medicine

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