UNIT 15.2 Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome

This unit focuses on some of the tools available on the public Galaxy server that are useful for exploring possible associations between human genetic variants and phenotypes. We trace step-by-step through an example illustrating several methods for examining a single full-coverage genome to look for single-nucleotide polymorphisms (SNPs) that are either known to be associated with disease or suspected to have impact for other reasons. It makes use of public genomic data, tools designed specifically for working with variants, and also some general tools for text manipulation and operations on genomic coordinates. Curr. Protoc. Bioinform. 39:15.2.1-15.2.27. © 2012 by John Wiley & Sons, Inc. Keywords: disease; SNP; genome variation; coding; non-coding; gene-based analysis; Web application