PCAtag

A tool to select tagging-SNPs (tSNPs). To comprehensively test the role of a candidate gene in an association study the selection of informative SNPs is paramount. Specifically, it is important to select tSNPs that represent a large portion (>90%) of the common genetic variation of a gene. PCAtag performs tSNP selection using principal component analysis (PCA) as described in Horne and Camp (2004). The advantage of PCA analysis for tSNP selection is that LD groups do not need to be contiguous and can be overlapping. This flexible framework does not impose over-simplified assumptions on the genetic architecture structure, and likely fits reality much better.