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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