BackgroundLow-pass sequencing followed by sequence variant genotype imputation is an alternative to the routine microarray-based genotyping in cattle. However, the impact of haplotype reference panels and their interplay with the coverage of low-pass whole-genome sequencing data have not been sufficiently explored in typical livestock settings where only a small number of reference samples is available.MethodsSequence variant genotyping accuracy was compared between two variant callers, GATK and DeepVariant, in 50 Brown Swiss cattle with sequencing coverages ranging from 4- to 63-fold. Haplotype reference panels of varying sizes and composition were built with DeepVariant based on 501 individuals from nine breeds. High-coverage sequence data for 24 Brown Swiss cattle were downsampled to between 0.01- and 4-fold to mimic low-pass sequencing. GLIMPSE was used to infer sequence variant genotypes from the low-pass sequencing data using different haplotype reference panels. The accuracy of the sequence variant genotypes that were inferred from low-pass sequencing data was compared with sequence variant genotypes called from high-coverage data.ResultsDeepVariant was used to establish bovine haplotype reference panels because it outperformed GATK in all evaluations. Within-breed haplotype reference panels were more accurate and efficient to impute sequence variant genotypes from low-pass sequencing than equally-sized multibreed haplotype reference panels for all target sample coverages and allele frequencies. F1 scores greater than 0.9, which indicate high harmonic means of recall and precision of called genotypes, were achieved with 0.25-fold sequencing coverage when large breed-specific haplotype reference panels (n = 150) were used. In absence of such large within-breed haplotype panels, variant genotyping accuracy from low-pass sequencing could be increased either by adding non-related samples to the haplotype reference panel or by increasing the coverage of the low-pass sequencing data. Sequence variant genotyping from low-pass sequencing was substantially less accurate when the reference panel lacked individuals from the target breed.ConclusionsVariant genotyping is more accurate with DeepVariant than GATK. DeepVariant is therefore suitable to establish bovine haplotype reference panels. Medium-sized breed-specific haplotype reference panels and large multibreed haplotype reference panels enable accurate imputation of low-pass sequencing data in a typical cattle breed.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12711-023-00809-y.