Size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle

Abstract

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 panel composition and its interplay with the coverage of low-pass whole-genome sequencing data has not been sufficiently explored in typical livestock settings where only a small number of reference samples are 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 considering 501 cattle from nine breeds. High coverage sequencing data of 24 Brown Swiss cattle was downsampled to between 0.01- and 4-fold coverage 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 imputed 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. Same-breed haplotype reference panels were better suited 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, implying 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 same-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 lacks individuals from the target breed. ConclusionsVariant genotyping is more accurate with Deep-Variant 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.