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.