SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium

Table 1 Number of pruned SNPs from the 52,843 SNPs present on the 60k pig SNP array

Analysis	One step^a	One step^a pre-sorted on MAF	Two step^a pre-sorted on MAF
Number of SNPs pruned out	Total	Total	High LD	Total^b
SNPrune	9126	9126	5296	9126
PLINK	9038	9098	5283	9113
Overlap^c	6792	6844	4939	8778

^aEither the LD pruning is done in one step, or in two steps, where 3830 SNPs in complete LD with other SNPs are removed in the first step, and the remaining SNPs in high LD are removed in the second step
^bIncluding the 3830 removed due to complete LD
^cOverlap between SNPs pruned by SNPrune and PLINK

ISSN: 1297-9686