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Table 2 Quality evaluation of variant detection using different variant-calling pipelines.

From: Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

  Sensitivity   Specificity
  Mean* SD Mean* SD
SOAPsnp 94.68 2.26 99.79 0.03
GATK1.5 95.34 1.16 99.72 0.08
SNVer 92.33 4.40 99.78 0.04
GNUMAP 86.60 3.23 99.64 0.06
SAMtools 94.47 4.22 99.59 0.16
Any pipeline 97.67 1.20 99.62 0.11
≥ 2 pipelines* 96.64 2.28 99.69 0.07
≥ 3 pipelines* 95.62 3.13 99.73 0.05
≥ 4 pipelines* 92.60 3.40 99.82 0.04
5 pipelines* 80.58 5.26 99.87 0.01
  1. *Intersection of variants contained in the number of pipelines specified.
  2. Sensitivity and specificity was calculated for each pipeline by comparing Illumina Human610-Quad version 1 SNP arrays with exome-capture sequencing results, based on the four samples whose genotyping data was available.