Table 4 Accuracy of sequence variant genotyping in low-coverage (1.11-fold) sequencing data
Variant genotyping approach | Genotype concordance | Non-reference sensitivity | Non-reference discrepancy |
|---|---|---|---|
GLIMPSE | 97.60 | 98.73 | 3.24 |
GATK raw | 75.90 | 52.35 | 30.20 |
GATK filtered | 75.89 | 52.36 | 30.22 |
GATK filtered & imputed | 85.74 | 96.56 | 19.34 |