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Breakdown of Methods for Phasing and Imputation in the Presence of Double Genotype Sharing

Figure 2

Comparison of switch error locations.

Switch errors for all markers for CEU trio parents on chromosome 21 plotted in order left-right, top-down ( markers). For each marker, red color intensity indicates the switch error rate for all 30 parents using the original MaCH 1.0.17 algorithm, while green intensity indicates the error rate using our proposed modification. Hence, yellow color indicates regions where errors are shared. The issue of bad chain mixing we describe for the original algorithm manifests as contiguous (horizontal) blocks of repeated switch errors using the original approach, while the error rate using the modified algorithm is 50% lower in total. The errors in the modified algorithm consist of events more evenly distributed. Several of those error locations coincide with errors from the original method. This figure also shows that even if overall haplotype quality in terms of error rate would be acceptable, some regions can still be heavily affected, and paradoxically those regions are the ones where multiple individuals share both haplotypes identical by descent.

doi: https://doi.org/10.1371/journal.pone.0060354.g002