Skip to main content

Table 2 Results of pipeline comparisons

From: Statistical method to compare massive parallel sequencing pipelines

  Parameter estimation
Variants, pipelines, and parameters Value [95% CI] [95% BVI]
All types of variants
 Regions sequenced by MPS onlya
  Number of variants for BWA-GATK 1857.14 [1789.27; 1927.58] [1461.16; 2360.43]
  Number of variants for TMAP-NextGENe 2253.49 [2149.96; 2361.99] [1660.16; 3058.86]
  OR for agreement 497.08 [464.55; 531.89] [323.36; 764.13]
  Conditional probability of identity 0.24 [0.23; 0.25] [0.20; 0.28]
 Regions sequenced by MPS and gold standardb
  Sensitivity of BWA-GATK (%) 63.47 [46.01; 87.55] [44.91; 89.69]
  Sensitivity of TMAP-NextGENe (%) 63.42 [45.95; 87.53] [44.68; 90.02]
  FP rate for 10,000 Sanger NV for BWA-GATK 43.03 [41.22; 45.20] NA
  FP rate for 10,000 Sanger NV for TMAP-NextGENe 35.25 [33.59; 36.80] NA
Only SNVs
 Regions sequenced by MPS onlya
  Number of SNVs for BWA-GATK 266.41 [259.17; 273.84] [232.84; 304.81]
  Number of SNVs for TMAP-NextGENe 314.24 [305.52; 323.21] [271.11; 364.24]
  OR for agreement 23289.85 [20226.42; 26817.25] [10099.35; 53708.09]
  Conditional probability of identity 0.9986 [0.9984;0.9989] NA
 Regions sequenced by MPS and gold standardb
  Sensitivity of BWA-GATK (%) 76.81 [63.50; 92.92] NA
  Sensitivity of TMAP-NextGENe (%) 76.81 [63.50; 92.92] NA
  FP rate for 10,000 Sanger NS for BWA-GATK 2.01 [1.82; 2.24] NA
  FP rate for 10,000 Sanger NS for TMAP-NextGENe 2.01 [1.82; 2.24] NA
  1. CI Confidence Interval, BVI Biological Variability Interval, OR Odds Ratio, FP False Positive, NV Non-variants, NS Non-SNVs
  2. a390,339 base-pairs per patient
  3. b1,085 to 16,570 base-pairs per patient