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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).