BMC Genomics

Table 4 Comparison of SWER, MEC and runtimes for SDhaP and CPLEX on simulated diploid data with 1% error rate

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

Data	Simulated data
	SDhaP			CPLEX(optimal)			CPLEX(heuristic)
	MEC	SWER	time	MEC	SWER	time	MEC	SWER	time
l 10³, c 10	100	0.001	1	100	0.001	192	100	0.001	57
l 10³, c 20	215	0.001	4	215	0.001	1320	215	0.001	373
l 10³, c 30	291	0.001	6	291	0.001	1241	291	0.001	910
l 10⁴, c 10	978	0.008	14	-	-	-	972	0.008	4505
l 10⁴, c 20	2039	0.004	33	-	-	-	2039	0.004	89811
l 10⁴, c 30	2988	0.004	68	-	-	-	-	-	-
l 10⁵, c 10	10356	0.008	324	-	-	-	-	-	-
l 10⁵, c 20	19975	0.007	713	-	-	-	-	-	-
l 10⁵, c 30	29967	0.005	1810	-	-	-	-	-	-

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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