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Table 4 Accuracy of sequence variant genotyping in low-coverage (1.11-fold) sequencing data

From: Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

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