In the final processing step we select LD tag SNPs. Because there are certain advantages to having functional and small P-value SNPs directly assessed by the genotyping panel (instead of being indirectly assessed via LD) we provide for the assignment of user-specified weights for different categories of functional SNPs and small P-value SNPs. If weights are assigned the null value of 1, then tag SNPs are selected simply by rank order, so that SNPs that are in high LD with the largest number of SNPs are selected first and SNPs that tag only themselves (singleton tags) are selected last. If a functional SNP has a weight applied, then the weight act as multiplier of the actual number of SNPs tagged so that it is more likely to be selected early. For example, a functional SNP with a weight of two 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
