Summary
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) 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
Using HapMap genotype data from ten ENCODE regions and design score distribution and fewer total tagSNPs selected by Snagger compared to the web server Tagger.
Snagger improves upon current available tagSNP software packages by providing a means for researchers to select tagSNPs that reliably capture genetic variation across multiple populations while accounting for significant genotyping failure risk and prioritizing on SNP-specific characteristics.
Haploview with Snagger has been developed and is maintained at the Genomics Center at the University of Southern California. For bug reporting, please refer to the project website: http://sourceforge.net/projects/snagger.
Citation
Snagger can be cited with the following article:
Edlund CK, Lee WH, Li D, Van Den Berg DJ, Conti DV. Snagger: A user-friendly program for incorporating additional information for tagSNP selection. BMC Bioinformatics. 2008 Mar 27; 9(1):174 [PubMed ID: 18371222]
http://www.biomedcentral.com/1471-2105/9/174