BMC Genomics

Table 3 Comparison of SWER, MEC and runtimes for different schemes on simulated diploid data

From: SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming

Data	Simulated data
	SDhaP			RefHap			HAPCUT			HapTree
	MEC	SWER	time	MEC	SWER	time	MEC	SWER	time	MEC	SWER	time
l 10³, c 10	86	0.002	4	123	0.009	8	123	0.009	6	123	0.009	31
l 10³, c 20	212	0.001	5	293	0.010	169	303	0.011	8	305	0.006	14
l 10³, c 30	300	0.001	7	378	0.007	567	377	0.002	7	378	0.001	14
l 10⁴, c 10	1112	0.003	28	1257	0.008	2341	1354	0.011	282	1354	0.010	34905
l 10⁴, c 20	2088	0.003	36	2659	0.008	36392	2774	0.009	680	2774	0.009	35443
l 10⁴, c 30	3482	0.004	81	4164	0.009	39184	4277	0.010	604	4283	0.009	17002

MEC, SWER and running times (in seconds) for SDhaP, RefHap, HAPCUT and HapTree algorithms for simulated data of different lengths (l) and with different coverages (c). The data contains a fixed 1% fraction of genotyping errors. SDhaP is more accurate in terms of MEC and SWER and faster by almost an order of magnitude compared to other schemes for longer blocks.

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ISSN: 1471-2164

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