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Snagger[1] is a bioinformatics software program for selecting tag SNPs using pairwise r2 linkage disequilibrium. It is implemented as extension to the popular software, Haploview,[2] and is freely available under the MIT License. Snagger distinguishes itself from existing single nucleotide polymorphism (SNP) selection algorithms, including Tagger,[3] 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) Selection of tagSNPs outside defined genomic regions to improve coverage and genotyping success

(4) 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.


  1. ^ Edlund CK, Lee WH, Li D, Van Den Berg DJ, Conti DV. "Snagger: A user-friendly program for incorporating additional information for tag SNP selection". BMC Bioinformatics. 2008 Mar 27; 9(1):174
  2. ^ Barrett J.C., Fry B., Maller J., Daly M.J. (2005). "Haploview: analysis and visualization of LD and haplotype maps". Bioinformatics 21: 263-265.
  3. ^ de Bakker P. I., Yelensky R., Pe'er I., Gabriel S. B., Daly M. J., Altshuler D. (2005). "Efficiency and power in genetic association studies.". Nature Genetics 37: 1217-1223.

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