FESTA (Fragmented Exhaustive Search for TAgSNPs) selects tagSNPs based on the pairwise LD measure r2. Using a pre-specified threshold d, it generates a tagSNP set such that every SNP is either in the tagSNP set itself or is in LD (with r2 > d ) with at least one SNP in the tagSNP set. This is an extension of the greedy approach proposed in Carlson et al. (2004). The basic idea is to partition the whole SNP set into disjoint precincts. Including or excluding certain SNPs, requiring double coverage of SNPs, as well as the original greedy approach (on disjoint precincts) are also included in this package.
Shyam Gopalakrishnan (email@example.com), Steve Qin @ the Center for Statistical Genetics
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Qin ZS, Gopalakrishnan S, Abecasis G
An effcient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria.
Bioinformatics (2006) 22 (2): 220-225.