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It's likely that those with low concordance genotypes might decrease imputation accuracies.
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The use of reference sequences that originate from the study sample itself can reduce the potential mismatch of ancestral backgrounds between sample and reference populations, decreasing imputation errors.
Among the pig autosomes, autosomes 10 and 12 had a relatively low average LD, which tends to decrease the length of shared haplotypes and therefore decreases imputation accuracy, since Beagle relies crucially on local LD structure [ 12].
It is expected that lower values for the scale and shift parameters will result in lower imputation error rates in most datasets, but the balance between decreasing imputation errors and longer computation times may lead to different optimal parameters in different datasets.
This decrease in imputation reliability follows the decay in LD, described as r dist 2, for Ne = 1000.
The sharp decrease in imputation accuracies when an external breed was used as reference population also supports that haplotypes are less conserved across breeds.
Our results suggest that LD-kNNi produces more accurate allele frequency estimates at the cost of a slight decrease in imputation accuracy.
Using the pre-phased HD data did not decrease the imputation accuracies (results not shown), but further studies are required to confirm these results as they include information from many more HD animals in the pre-phasing which could improve the phasing quality, thus making them not directly comparable.
Pre-phasing the reference data only lead to a minor decrease in the imputation accuracy, but gave a large improvement in computation time.
Results are presented for four combinations of method and dataset: method A, B, and C applied to dataset 1, and method C applied to dataset 2. For classes of animals with traceability above 0.50, there was a clear decrease in the imputation error rate with increasing traceability.
Impute: impute: Imputation for microarray data.
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