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

BMC Bioinformatics

Table 3 Comparison of running time and number of tag SNPs selected when multi-marker LD are used.

	*max_size*	*min_r* 2	Running time (minutes)				#tag SNPs
			Fast-COOC	MMTagger	Fast-1vsR	MultiTag	Fast-COOC	MMTagger	Fast-1vsR	MultiTag
ENCODE CEU	2	0.95	0.038	0.041	0.048	≥10 hours	1282	1282	1291	1371
ENCODE HCB	2	0.95	0.032	0.032	0.042	≥10 hours	1305	1328	1308	1424
ENCODE JPT	2	0.95	0.029	0.028	0.038	≥10 hours	1234	1258	1240	1349
ENCODE YRI	2	0.95	0.181	0.188	0.245	≥60 hours	2575	2618	2579	2770
chr1	2	0.95	1.13	5.84	1.40	≥7 days	43202	43483	43306	43462
chr2	2	0.95	1.32	7.21	1.63	≥7 days	44135	44556	44225	49289
chr3	2	0.95	1.14	5.11	1.41	≥7 days	37881	38206	37952	39300
chr19	2	0.95	0.176	0.343	0.218	≥30 hours	11151	11192	11160	11747
chr21	2	0.95	0.287	0.473	0.359	≥60 hours	8543	8627	8564	9103
chr22	2	0.95	0.370	0.567	0.468	≥100 hours	8970	9025	8993	9533
ENCODE CEU	3	0.95	1.28	3.69	1.85	≥50 hours	972	1017	1151	1244
ENCODE HCB	3	0.95	1.26	3.40	1.93	≥80 hours	1003	1034	1170	1170
ENCODE JPT	3	0.95	1.06	2.74	1.60	≥50 hours	958	1002	1129	1244
ENCODE YRI	3	0.95	11.6	36.7	17.4	≥14 days	1848	1927	2165	2516
chr1	3	0.95	34.9	137.3	49.6	-	35556	38185	40534	-
chr2	3	0.95	42.9	166.9	60.8	-	35502	38372	41129	-
chr3	3	0.95	39.3	154.6	55.5	-	30695	33041	35305	-
chr19	3	0.95	4.34	16.6	6.25	-	9444	10032	10546	-
chr21	3	0.95	9.91	37.7	14.4	-	6929	7404	7935	-
chr22	3	0.95	16.5	65.3	24.4	-	7327	7788	8392	-

Fast-COOC represents the FastTagger algorithm using the co-occurrence model, and Fast-1vsR represents the FastTagger algorithm using the one-vs-the-rest model. max_size is the maximum number of SNPs on the left hand side of a tagging rule. For the MMTagger algorithm, we divided chr1, chr2 and chr3 into 10 chunks when max_size = 3, and ran MMTagger on each chunk, and then combined the results. For the MultiTag algorithm, we divided chr1, chr2 and chr3 into 20 chunks, chr19, chr21 and chr22 into 5 chunks when max_size = 3. When max_size = 3, MultiTag took too long to finish on the 6 chromosomes, so we did not get its results on the 6 chromosomes.

ISSN: 1471-2105