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Table 1 Variant calling sensitivity and specificity for the consensus 3of4 approach ensures high specificity and FDR without a loss of sensitivity

From: A hybrid computational strategy to address WGS variant analysis in >5000 samples

  Consensus 3of4 Consensus 2of4 GATK-HC GATK-UG GotCloud SNPTools
# SNVs 72,945,834 86,233,412 103,439,411 104,649,069 78,483,824 66,290,585
Ti/Tv 2.12 2.08 2.00 2.00 2.09 1.99
% in 1000G 50.22 % 43.75 % 36.35 % 36.54 % 46.91 % 51.17 %
% in dbSNP 40.25 % 35.31 % 28.88 % 29.53 % 37.93 % 41.91 %
sensitivity 63.80 % 68.98 % 68.51 % 69.99 % 64.17 % 51.26 %
specificity 99.92 % 99.70 % 99.30 % 99.54 % 99.86 % 99.13 %
FDR 3.34 % 11.29 % 22.91 % 16.16 % 6.12 % 33.11 %
  1. The gold standard dataset consists of 4612 samples with 80–100 × coverage. All the four callers are necessary for increasing the yield of SNVs