Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle.

ABSTRACT:

Background

The advent of low cost next generation sequencing has made it possible to sequence a large number of dairy and beef bulls which can be used as a reference for imputation of whole genome sequence data. The aim of this study was to investigate the accuracy and speed of imputation from a high density SNP marker panel to whole genome sequence level. Data contained 132 Holstein, 42 Jersey, 52 Nordic Red and 16 Brown Swiss bulls with whole genome sequence data; 16 Holstein, 27 Jersey and 29 Nordic Reds had previously been typed with the bovine high density SNP panel and were used for validation. We investigated the effect of enlarging the reference population by combining data across breeds on the accuracy of imputation, and the accuracy and speed of both IMPUTE2 and BEAGLE us

SUBMITTER: Brondum RF 

PROVIDER: S-EPMC4152568 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature