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Table 1 Number of variants identified by the pipelines and by the gold standard in N patients

From: Statistical method to compare massive parallel sequencing pipelines

Variants and pipelines

N

Mean ± SD

Min.

Q1

Median

Q3

Max.

All types of variantsa

 Regions sequenced by MPS onlyb

       

  BWA-GATK

43

1871 ± 225.08

1198

1696

1867

2056

2360

  TMAP-NextGENe

43

2280 ± 339.72

1214

2014

2256

2504

3094

 Regions sequenced by MPS + gold standardb

       

  Sanger

30

2.67 ± 2.88

0

1

1

3.75

10

  BWA-GATK

30

27.40 ± 20.54

3

10.50

25

36

92

  TMAP-NextGENe

30

22.77 ± 18.71

3

9.25

17

28

75

SNVs only

 Regions sequenced by MPS onlya

       

  BWA-GATK

43

267 ± 22.04

204

251.50

267

280

318

  TMAP-NextGENe

43

315.10 ± 28.32

215

302.50

317

334

384

 Regions sequenced by MPS + gold standardb

       

  Sanger

30

2.30 ± 2.79

0

0

1

3

9

  BWA-GATK

30

2.77 ± 2.81

0

1

2

4

10

  TMAP-NextGENe

30

2.77 ± 2.81

0

1

2

4

10

  1. aSingle Nucleotide Variants (SNVs), insertions, and deletions
  2. b390,339 base-pairs per patient
  3. c1,085 to 16,570 base-pairs per patient