BMC Proceedings

Table 2 Random selection of 200 reference/dense SNP panel individuals

From: Identity-by-descent estimation with population- and pedigree-based imputation in admixed family data

	(0–0.01]: #SNPs = 4604 SNPs			(0.01–0.15]: #SNPs = 1765 SNPs			(0.15–0.5]: #SNPs = 979 SNPs
Imputation approaches	#SNPe	ρ₁	ρ₂	#SNPe	ρ₁	ρ₂	#SNPe	ρ₁	ρ₂
BEAGLE-BEAGLE	4325	0.209	0.196	1673	0.587	0.556	976	0.897	0.895
SHAPEITped-BEAGLE	4554	0.270	0.267	1763	0.730	0.729	979	0.978	0.978
MaCH-MaCH	4388	0.332	0.316	1755	0.595	0.591	979	0.801	0.801
MaCH-minimac	4523	0.460	0.452	1763	0.706	0.706	979	0.910	0.910
SHAPEITped-minimac	4507	0.642	0.629	1765	0.894	0.894	979	0.985	0.985
MaCH-MaCHAdmix	4340	0.420	0.396	1754	0.687	0.683	979	0.896	0.896
SHAPEITped-MaCHAdmix	4352	0.527	0.498	1760	0.773	0.770	979	0.904	0.904
GIGI	3763	0.610	0.498	1719	0.557	0.542	979	0.581	0.581
IMPUTE2-IMPUTE2	4230	0.370	0.340	1735	0.660	0.649	978	0.898	0.897
SHAPEITped-IMPUTE2	4401	0.485	0.464	1741	0.713	0.703	979	0.923	0.923
GIGI + SHAPEITped-BEAGLE	4507	0.643	0.630	1764	0.790	0.789	979	0.972	0.972
GIGI + SHAPEITped-minimac	4507	0.693	0.678	1764	0.860	0.860	979	0.980	0.980
GIGI + SHAPEITped-IMPUTE2	4491	0.635	0.619	1746	0.740	0.732	979	0.876	0.876

#SNPs is the total number of SNPs in the reference panel; #SNPe is the number of imputed SNPs as polymorphic; ρ₁ is the mean correlation of all SNPs: sum(correlation)/#SNPe; ρ₂ = sum(correlation)/#SNPs

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ISSN: 1753-6561

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