BMC Bioinformatics

Table 2 Comparison of running time and number of tag SNPs selected when pairwise LD are used.

From: FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium

	*min_r* 2	Running time (minutes)			#tag SNPs
		FastTagger	LRTag	MultiTag	FastTagger	LRTag	MultiTag
ENCODE CEU	0.95	0.003	0.016	10.4	2144	2127	2136
ENCODE HCB	0.95	0.003	0.014	7.5	2065	2055	2061
ENCODE JPT	0.95	0.003	0.013	6.6	1996	1990	1996
ENCODE YRI	0.95	0.004	0.008	41.6	4115	4107	4109
chr1	0.95	0.076	0.242	26.2	62190	61988	63391
chr2	0.95	0.088	0.293	30.2	66026	65822	67236
chr3	0.95	0.070	0.222	25.1	55895	55713	56972
chr19	0.95	0.015	0.032	3.6	14777	14744	15014
chr21	0.95	0.015	0.040	6.0	12455	12435	12658
chr22	0.95	0.014	0.033	7.9	12690	12652	12932

The running time of LRTag includes only tag SNP selection time, while the running time of FastTagger and MultiTag includes both rule generation time and tag SNP selection time. MMTagger is excluded from this table because the MMTagger program provided by its authors cannot use pairwise LD to find tag SNPs.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com