that is in LD with four SNPs (including itself) would have a weighted tag value of 2 × 4 = 8. Investigators may modify a variety of values (e.g. P-value threshold T1, LD threshold, or weights) to adjust selected SNP counts to fit their genotyping panel size and budget. We provide two options for additional SNP reduction that we think are useful: (i) Each SNP must be in LD with a user-specified minimum number of common SNPs (after multiplied by the user-assigned weights). For example, this option can be used to eliminate singleton SNPs. (ii) A user can also specify the maximum number of SNPs that are allowed for any one gene using a method which is similar to selecting the best N SNPs to optimize power (7). To insure that each gene has some coverage, we also provide a user-specified minimum number of best SNPs (in terms of number of SNPs captured at a specific LD threshold) that must be selected for each gene even if they do not meet the previous criterion for tag SNPs.
