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Long-range switch error measurements were obtained using BAC end sequences.
The long-range switch error rate was calculated as: no. of long range switches/no. of phasing markers.
However, such two contiguous switch error disrupt twice in terms of switch error rate (bottom of Figure 2(B)).
A single switch error in the middle of a gene would drop phase accuracy to zero, as would a switch error between every pair of markers.
In 2011, we introduced the concept of a smoothed switch error, and a declining relationship of switch error as a function of lowering the high-frequency cutoff [ 8].
The switch error rate improved after removing suspicious CFs in all conditions.
Similar(7)
Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster.
However, inclusion of all of the homozygous markers will increase the switch-error denominator and reduce the metric.
A common metric is the switch-error rate, sometimes known as phase error, switch accuracy, or recast (reformulated) as switch distance.
Switch-error rate: The proportion of heterozygous sites in each reconstructed haplotype that are mis-assigned relative to the heterozygous site that directly precedes it.
In its usual form, the switch-error rate is identical for a single base error (two switches very close together) or for two switches on different arms of a chromosome (two switches very far apart).
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