Best practices for genotype imputation from low-coverage sequencing data in natural populations.

ABSTRACT: Monitoring genetic diversity in wild populations is a central goal of ecological and evolutionary genetics and is critical for conservation biology. However, genetic studies of nonmodel organisms generally lack access to species-specific genotyping methods (e.g. array-based genotyping) and must instead use sequencing-based approaches. Although costs are decreasing, high-coverage whole-genome sequencing (WGS), which produces the highest confidence genotypes, remains expensive. More economical reduced representation sequencing approaches fail to capture much of the genome, which can hinder downstream inference. Low-coverage WGS combined with imputation using a high-confidence reference panel is a cost-effective alternative, but the accuracy of genotyping using low-coverage WGS and imputation

SUBMITTER: Watowich MM 

PROVIDER: S-EPMC10879460 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature