Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees

Table 3 Median imputation accuracy for non-sequenced individuals as a function of used sequencing datasets and individual’s SNP array genotype status for (a) all non-sequenced individuals or (b) the final four quintiles of the population

	High density	Low density	No genotype
(a) All individuals
Focal	0.967	0.936	0.855
Focal and low coverage sires	0.983	0.952	0.863
Focal and all low coverage (all sequenced)	0.987	0.971	0.881
findhap with all sequenced	0.958	0.892	0.702
(b) Final four quintiles
Focal	0.968	0.968	0.939
Focal and low coverage sires	0.984	0.985	0.953
Focal and all low coverage (all sequenced)	0.987	0.988	0.959
findhap with all sequenced	0.959	0.916	0.765

ISSN: 1297-9686