Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle.

ABSTRACT:

Background

Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required.

Results

In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes

SUBMITTER: Frischknecht M 

PROVIDER: S-EPMC5747239 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature