Empirical vs Bayesian approach for estimating haplotypes from genotypes of unrelated individuals

BMC Genomic Data

Table 4 Performances of haplotyping programs on simulated data based on a coalescence model with mutation rate of 4 (= 4N_eθ).

Average #SNP	Sample size	Similarity Index				Prediction Rate				Average Running Time (in seconds)
		Empirical		Bayesian		Empirical		Bayesian		Empirical		Bayesian
		PL-EM	Hplus	PHASE	HAPLO⁺	PL-EM	HPlus	PHASE	HAPLO⁺	PL-EM	HPlus	PHASE	HAPLO⁺
25	100	0.943	0.947	0.982	0.976	0.941	0.945	0.981	0.976	1.39	0.18	122.89	2.52
25	150	0.955	0.960	0.988	0.986	0.952	0.957	0.988	0.986	2.56	0.23	185.86	3.09
26	200	0.967	0.971	0.991	0.988	0.964	0.968	0.988	0.988	5.51	0.29	283.28	4.36
29	250	0.974	0.977	0.992	0.986	0.973	0.976	0.993	0.980	12.37	0.36	429.03	5.75

ISSN: 2730-6844