Statistical method to compare massive parallel sequencing pipelines

BMC Bioinformatics

Table 2 Results of pipeline comparisons

	Parameter estimation
Variants, pipelines, and parameters	Value	[95% CI]	[95% BVI]
All types of variants
Regions sequenced by MPS only^a
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 standard^b
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 only^a
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 standard^b
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

CI Confidence Interval, BVI Biological Variability Interval, OR Odds Ratio, FP False Positive, NV Non-variants, NS Non-SNVs
^a390,339 base-pairs per patient
^b1,085 to 16,570 base-pairs per patient

ISSN: 1471-2105