Snagger: A user-friendly program for incorporating additional information for tagSNP selection

Background: There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important. Results: We have developed a user-friendly and efficient software program, Snagger, as an extension to the existing open-source software, Haploview, which uses pairwise r2 linkage disequilibrium between single nucleotide polymorphisms (SNPs) to select tagSNPs. Snagger distinguishes itself from existing SNP selection algorithms, including Tagger, by providing user options that allow for: (1) prioritization of tagSNPs based on certain characteristics, including platform-specific design scores, functionality (i.e., coding status), and chromosomal position, (2) efficient selection of SNPs across multiple populations, (3) sele...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Christopher K. Edlund, Won H. Lee, Dalin Li, David J. Van Den Berg, David V. Conti
• Keywords: BMCBI 2008, Design Score, Single Nucleotide Polymorphisms, SNPs