. Author manuscript; available in PMC: 2011 Apr 1.

Published in final edited form as: Genet Epidemiol. 2010 Apr;34(3):258–265. doi: 10.1002/gepi.20457

TABLE VI.

Linkage disequilibrium-based SNP pruning for HapMap phase III reference panels

Phase III Reference Panel	Founders	Retained SNPs
ASW	49	1,947
CEU	112	1,432
CEU	49	1,138.3
YRI	113	2,886
YRI	49	2,038.2

For the CEU and YRI reference panels, 49 founders were randomly sampled from the available founders. Shown are averages from 30 randomly generated data sets.

The number of retained SNPs was determined using the --indep-pairwise function in PLINK, with a window size of 100 SNPs, a step of 25 SNPs, and a maximum r² threshold of 0.2.