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

ABSTRACT:

Background

Low-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.

Methods

Sequence 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

SUBMITTER: Lloret-Villas A 

PROVIDER: S-EPMC10173671 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature