Owing to the 4-fold increase in the size of the reference multi-genome alphabet, the BWBBLE program performs many more SA interval computations, which causes its running time to be significantly slower.
Note that although augmenting the reference with indels and other structural variants allows us to easily handle these events during alignment, it does lead to an increase in the size of the reference string due to padding and, therefore, a higher memory overhead.
For those reasons, it is important to investigate when GS offers advantages over traditional selection in cases in which the size of the reference population is limited.
Although it is reasonable to let the reference ortholog set consist of nodes in CCNs, the size of the reference set should be chosen appropriately because large reduction of dimensions may cause the correlation values to be unreliable while a too large size makes the performance of Essien et al.'s method approach that of Dutilh et al.'s method.
In fact, the size of the reference population had a limited effect when the number of HD genotypes was greater than a minimum threshold that was estimated at 200 400 animals.
As a consequence, small reductions in generation interval lead to relatively large reductions in the break-even size of the reference population.
This plateau in coverage may be in part due to the limited size of the reference sample, and in part due to the underlying structure of the genome being such that some regions have insufficient LD to accurately impute variants, regardless of MAF.
In order to determine an optimal size of the reference area, various distances in latitude and longitude are compared such as 0.1°, 0.2°, and 0.3°.
The figures also show a slight increase in imputation performance as the size of the reference panel increased.
Age structure is different in the four datasets, so we took different age thresholds for different datasets based on the principle that the reference group should consist of relatively younger patients in each dataset and sample size of the reference group should not be too small.
