Imputation accuracy of whole-genome sequence data in Hanwoo cattle This study reports the accuracy of imputation to whole genome sequence (WGS) from lower density genotype data in Korean Hanwoo cattle. A total of 203 reference Hanwoo cattle were used to impute 4,887 animals genotyped with Illumina BovineSNP50 v2 (50k). Also, a set of 928 animals genotyped with Illumina BovineHD chip (HD, 770k) were used as an intermediate reference dataset. First, the animals were imputed from 50k to HD and then imputed from HD to sequence. The accuracy of imputation was evaluated in animals in common between the reference and imputed population. Haplotype phasing and imputation was done using Eagle2 and Minimac3 software respectively. The imputation accuracy was calculated as the correlation between the imputed and observed genotypes and also as the percentage of correctly imputed genotypes (concordance rate). We achieved a mean imputation accuracy of 0.97 from 50k to WGS. The imputed data is useful to explore GWAS and genomic prediction for different commercially important traits in the Korean Hanwoo cattle. Keywords: Hanwoo cattle, imputation accuracy, whole genome sequence data
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Methods and Tools - Imputation, , 735, 2018
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