Snagger (software)

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

References

  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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