Snagger (software)

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Snagger is a bioinformatics software program for selecting tag SNPs using pairwise r² linkage disequilibrium.Edlund CK, Lee WH, Li D, Van Den Berg DJ, Conti DV. "[http://www.biomedcentral.com/1471-2105/9/174 Snagger: A user-friendly program for incorporating additional information for tag SNP selection]". BMC Bioinformatics. 2008 Mar 27; 9(1):174 It is implemented as extension to the popular software, Haploview, and is freely available under the MIT License.Barrett J.C., Fry B., Maller J., Daly M.J. (2005). "[https://web.archive.org/web/20060517184621/http://bioinformatics.oxfordjournals.org/cgi/reprint/21/2/263?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Haploview&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Haploview: analysis and visualization of LD and haplotype maps]". Bioinformatics 21: 263-265. Snagger distinguishes itself from existing single nucleotide polymorphism (SNP) selection algorithms, including Tagger,de Bakker P. I., Yelensky R., Pe'er I., Gabriel S. B., Daly M. J., Altshuler D. (2005). "[http://www.nature.com/ng/journal/v37/n11/pdf/ng1669.pdf Efficiency and power in genetic association studies].". Nature Genetics 37: 1217-1223. by providing user options that allow for:

• Prioritization of tagSNPs based on certain characteristics, including platform-specific design scores, functionality (i.e. coding status), and chromosomal position
• Efficient selection of SNPs across multiple populations
• Selection of tagSNPs outside defined genomic regions to improve coverage and genotyping success
• Picking of surrogate tagSNPs that serve as backups for tagSNPs whose failure would result in a significant loss of data

Haploview with Snagger has been developed and is maintained at the Genomics Center at the University of Southern California.