Comparison of Genotype Imputation for SNP Array and Low-Coverage Whole-Genome Sequencing Data.

ABSTRACT: Genotype imputation is the term used to describe the process of inferring unobserved genotypes in a sample of individuals. It is a key step prior to a genome-wide association study (GWAS) or genomic prediction. The imputation accuracy will directly influence the results from subsequent analyses. In this simulation-based study, we investigate the accuracy of genotype imputation in relation to some factors characterizing SNP chip or low-coverage whole-genome sequencing (LCWGS) data. The factors included the imputation reference population size, the proportion of target markers /SNP density, the genetic relationship (distance) between the target population and the reference population, and the imputation method. Simulations of genotypes were based on coalescence theory accounting for the demo

SUBMITTER: Deng T 

PROVIDER: S-EPMC8762119 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature