multiPopTagSelect attempts to select a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations. Specifically, it processes the output of tagSNP selection algorithms that designate bins of nearly equivalent SNPs, such that choosing (and typing) one SNP from each bin is sufficient to capture all associations observed in the data. Most of this documentation concerns one particular tagSNP selection method known as ldSelect, but multiPopTagSelect can also be used with other methods whose output has been converted into ldSelect format. This program can optimize SNP selection across any number of populations, and it can be applied to genomic regions ranging from small genes to entire chromosomes.
Dr. Deborah Nickerson’s lab at the University of Washington
- Linux / Windows / Max OS X
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Howie BN, Carlson CS, Rieder MJ, Nickerson DA. Efficient selection of tagging single-nucleotide polymorphisms in multiple populations. Hum Genet. 2006 120(1):58-68.