SNP-PHAGE: high-throughput SNP discovery pipeline.

High-throughput genotyping technologies have become popular in studies that aim to reveal the genetics behind polygenic traits such as complex disease and the diverse response to some drug treatments. These technologies utilize bioinformatics tools to define strategies, analyze data, and estimate the final associations between certain genetic markers and traits. The strategy followed for an association study depends on its efficiency and cost. The efficiency is based on the assumed characteristics of the polymorphisms' allele frequencies and linkage disequilibrium for putative casual alleles. Statistically significant markers (single mutations or haplotypes) that cause a human disorder should be validated and their biological function elucidated. The aim of this chapter is to present a subset of bioinformatics tools for haplotype inference, tag SNP selection, and genome-wide association studies using a high-throughput generated SNP data set.