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Sequence data can be used in genomic selection (GS), genome-wide association studies (GWAS) and the analysis of recessive lethal defects instead of, or complementary to, SNP array genotypes and increase the power of those applications in various ways. Because sequencing large study cohorts is still expensive, genotype imputation - the prediction of missing genotypes - is a cost-effective alternative to generate sequence-level genotypes for a large number of animals. These genotypes can then be used in subsequent studies and, for example, facilitate the identification of causative mutations. In this context, it is important to consider the accuracy of imputation and to know the factors affecting it. As the availability of sequence data from (warmblood) horses is limited, for this species, imputation is a good possibility to generate sequence level genotypes, which can boost the power of GWAS and the identification of recessive lethal defects. [ABSTRACT FROM AUTHOR]