Table 2 Summary of retrospective variant analysis.

From: Reducing Sanger confirmation testing through false positive prediction algorithms

Variant/genotype

Confirmed true calls

False calls

False calls captured

True calls flagged

Model TP flag rate

SNV—heterozygous

176

0

—

29 (16.48%)

12.20%

SNV—homozygous

34

0

—

1 (2.94%)

17.40%

SNV—complex heterozygous

0

0

—

—

—

Indel—heterozygous

20

2

2 (100.00%)

5 (25.00%)

43.41%

Indel—homozygous

0

0

—

—

55.16%

Indel—complex heterozygous

0

0

—

—

54.22%

  1. Here we report the total number of variants confirmed to be true positive (TP) or false positive calls, the number of false positive calls correctly identified (capture rate), and the number of true calls incorrectly labeled as false calls (TP flag rate). The model TP flag rate (i.e., expected TP flag rate) from the final evaluation is also provided here for comparison. Models used for this analysis were generated from the Dragen-based pipeline.
  2. SNV single-nucleotide variant.
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