Table 1 Variant calling performance for pharmacogenes.

From: Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle

Variant caller

SNVs

Indels

Precision (%)

Recall (%)

F1 (%)

Precision (%)

Recall (%)

F1 (%)

GATK haplotype caller

99.88

99.96

99.92

94.47

86.12

90.10

DeepVariant (CCS model)

99.84

100.0

99.92

98.74

98.00

98.37

  1. Measured against the Genome in a Bottle benchmark v.3.3.2. using both GATK variant caller and DeepVariant. SNV single nucleotide variant, Indels insertions and deletions, GATK genomic analysis toolkit, CCS circular consensus sequence.
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