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

BMC Bioinformatics

Table 5 Comparison of the estimated running times of various software on 300 K Illunima genotyping chips datasets.

#SNPs	#genotypes	Fastphase	Ishape	Shape-IT	Phase v2.1
50	100	10	29	10	151
100	100	6	37	12	519
200	100	6	41	19	3,137
50	200	21	34	13	443
100	200	21	119	29	2,739
200	200	21	124	37	7,601
50	300	37	113	28	1,372
100	300	41	268	52	6,514
200	300	42	261	81	12,757

Estimations of the running times in days of the 4 most accurate software (Phase v2.1, Ishape, Fastphase and Shape-IT) to infer the haplotypes for 100, 200, or 300 genotypes derived from Illumina 300 k chips partitioned into segments of either 50 SNPs, or 100 SNPs, or 200 SNPs. For each combination #SNPs #genotypes, the running time estimations were extrapolated from the measures performed on 10 datasets extracted from the GRIV cohort 300 K Illumina chip genomic data.