Software programs FImpute and BEAGLE were applied to impute genotypes.  FImpute outperformed BEAGLE for all LD chips and validation sets.  If the Illumina® BovineHD is considered as the target chip for genomic applications in the Nelore breed, cost-effectiveness can be improved by genotyping part of the animals with a chip containing around 15 K useful SNPs and imputing their high-density missing genotypes with FImpute.
FImpute
Software programs FImpute and BEAGLE were applied to impute genotypes.  FImpute outperformed BEAGLE for all LD chips and validation sets. 
BEAGLE