PEDIMPUTE: Imputing genotypes using a fast algorithm combining pedigree and population information
Keywords:
SNP, imputation, Holstein, dairy cattleAbstract
Routine genomic evaluations frequently include a preliminary imputation step, requiring high accuracy and reduced computing time. A new algorithm, namely PEDIMPUTE, was developed and compared to FINDHAP algorithm using 6662 genotypes from the Italian Holstein population. Different scenarios were evaluated creating two subsets including only SNPs from the Bovine 3k and LD Illumina BeadChip, respectively. The comparative criteria were % missing alleles, % of wrongly imputed alleles, and the allelic squared correlation. PEDIMPUTE was slightly more accurate and faster than FINDHAP in almost all scenarios. Error rate and allelic squared correlation attained by PEDIMPUTE ranged from 0.2 to 3.7 % and from 88.6 to 99.3 %, respectively.
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