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 |