Identity-by-descent graphs offer a flexible framework for imputation and both linkage and association analyses

BMC Proceedings

Table 1 Design of imputation experiments

		Subjects with observed marker data¹		GIGI	BEAGLE
Family	Subject status	Design 1	Design 2		F10 + FO	F10	FO
		Number of subjects		Number of variants observed per subject
Family 10	Typed	44	15	65,403	65,403	65,403	0
	Masked	20	49	351²	3621³	3621³	36213
Others	Typed	308	308	0	65,403	0	65,403

¹Original genome-wide association studies genotypes are observed or masked for the imputation markers as per subject status.
²Framework markers on chromosome 3 used to sample identity-by-descent (IBD) graphs.
³Dense scaffold markers used by BEAGLE to infer IBD. Scaffold markers include the framework markers.

ISSN: 1753-6561