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The aim of this study was to investigate the accuracy and speed of imputation from a high density SNP marker panel to whole genome sequence level.
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We investigated the effect of enlarging the reference population by combining data across breeds on the accuracy of imputation, and the accuracy and speed of both IMPUTE2 and BEAGLE using either genotype probability reference data or pre-phased reference data.
Section 5 explains how to further speed up the imputation of the CG by selecting a subset of the CG dynamically.
Sensitivity of imputation method: An imputation method is required for the derivation of PE.
(We discuss choice of imputation models and the number of imputations later in this paper).
Rates of imputation varied within and between states.
Effects of imputation grain and heterogeneous plots on map accuracy were small.
And, as has recently come to light, there was a lot of imputation (a fancy statistical term for educated guessing) going on in the WHO data.
Missing value imputation was undertaken using the method of imputation by chained equations [36].
Interestingly, imputation accuracy is nearly the same for EA as for AA, again highlighting how imputation accuracy can overestimate the quality of imputation.
However, with respect to imputation speed, NI imputation was the fastest, while RF imputation was extremely slow.
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CEO of Professional Science Editing for Scientists @ prosciediting.com