Computational protocol: Accuracy of genotype imputation based on random and selected reference sets in purebred and crossbred sheep populations and its effect on accuracy of genomic prediction

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Protocol publication

[…] The Beagle software program v3.2 [] was used to impute un-typed genotypes in the test set. Imputation was performed separately for each chromosome and was based on 10 iterations. The accuracy of imputation was calculated for each individual in the test set as the Pearson correlation coefficient between observed and imputed 50k genotypes, after discarding the 12k observed genotypes. If imputation was based on a selected reference set, imputation accuracies were also based on the Pearson correlation coefficient of each imputed SNP across test individuals, as well as on the Pearson correlation coefficient between imputed and observed genotypes for each test individual. […]

Pipeline specifications

Software tools BEAGLE, IMPUTE
Application GWAS
Organisms Ovis aries