Shape-IT: new rapid and accurate algorithm for haplotype inference

BMC Bioinformatics

Table 4 Hapmap trio datasets results

Datasets	Shape-IT		Phase v2.1		Fastphase		Ishape		2snp		Gerbil		PLEM
	SER	Time	SER	Time	SER	Time	SER	Time	SER	Time	SER	Time	SER	Time
CEU Size	*1.1*		*1.1*		1.5		1.1		2.2		2.3		2.0
		53		832		113		93		< 1		50		10
YRI Size	*1.7*		*1.7*		2.3		1.8		4.5		3.9		4.2
		64		1,209		125		138		< 1		131		10
CEU Density	*2.3*		*2.3*		2.7		2.4		4.2		4.0		4.1
		26		214		64		43		< 1		5		6
YRI Density	*3.7*		*3.7*		4.9		3.9		8.5		7.5		8.8
		35		490		71		80		< 1		9		5
CEU MAF	*1.1*		*1.1*		1.2		1.2		2.0		2.1		1.7
		19		104		71		22		< 1		2		4
YRI MAF	*1.5*		*1.5*		2.0		*1.5*		4.5		3.8		3.2
		26		173		80		38		< 1		4		4
CEU 50 illumina SNP	*6.3*		*6.3*		7.2		6.6		10.7		9.2		12.2
		51		1,214		60		161		< 1		22		5
CEU 100 illumina SNP	*6.7*		6.8		7.7		9.2		11.3		9.7		N/A
		143		11,678		144		461		< 1		254		N/A
CEU 200 illumina SNP	*7.2*		N/A		8.0		N/A		11.5		9.9		N/A
		372		N/A		198		N/A		< 1		2,038		N/A

N/A: software was unable to handle some of these datasets (errors or untracktable running times). Results of the various tested software on the HapMap trios datasets described in Table 1. For each software tested, the mean percentage of heterozygous markers incorrectly inferred (SER) is shown in the upper-left corner, and the mean running time in seconds is shown in the lower-right corner.

ISSN: 1471-2105