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Table 2 Sensitivity and specificity of WES genotypes for exome array genotypes in 10 samples

From: Effective filtering strategies to improve data quality from population-based whole exome sequencing studies

Filters TP1 TN2 FP3 FN4 Sensitivity TP/(TP+FN) Specificity TN/(TN+FP)
Genotype Variant
None None 73,537 621,855 661 551 99.26% 99.89%
None VQSR 73,069 608,065 108 493 99.33% 99.98%
DP None 72,104 611,606 627 236 99.67% 99.90%
GQ None 72,689 610,682 460 225 99.69% 99.92%
DP & GQ None 71,986 610,108 446 220 99.70% 99.93%
DP & GQ VQSR 71,552 597,070 36 168 99.77% 99.99%
  1. 1TP = exact match of non-reference genotype; Ref/Alt with Ref/Alt or Alt/Alt with Alt/Alt.
  2. 2TN = exact match of reference genotype; Ref/Ref with Ref/Ref.
  3. 3FP = additional alternate allele in WES genotype; Ref/Ref with Ref/Alt or Ref/Ref with Alt/Alt or Ref/Alt with Alt/Alt.
  4. 4FN = missing alternate allele in WES genotype; Ref/Alt with Ref/Ref or Alt/Alt with Ref/Ref or Alt/Alt with Ref/Alt.
  5. (See Additional file 3).