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

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

#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
  1. 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.