TAGster

TAGster: Single or Multi-Population Tag SNPs Selection, Evaluation and Visualization

TAGster is a tool to select, evaluate and visualize LD tag SNPs for single or multiple populations. The input files can be a set of dumped genotype files from International HapMap Project (http://www.hapmap.org/) (Hapmap format) or Seattle SNPs (http://pga.gs.washington.edu/) (Prettybase format). The ouput is a set of LD tag SNPs for single or multiple populations.

The TAGster also creates figures for LD structure and genotype data with many customized tracks to facilitate investigators visually checking and optimizing tag SNPs.

The TAGster uses composite linkage disequilibrium (CLD) coefficient or r² to measure patterns of linkage disequilibrium between polymorphic sites in a genome region within each of multiple populations, and employs 3 methods to select LD tag SNPs:

1. A greedy algorithm to select a set containing a near-minimal number of LD tag SNPs for a single or multiple populations
2. A computation efficient exhaustive method to select minimal number of tag SNPs for a single population
3. A two-stage optimal method to select a set of near-minimal number of tag SNPs for multiple populations

Downloads

• Windows Binary: tagster_win.zip (http://www.niehs.nih.gov/research/resources/software/tagster/docs/tagster_win.zip)   (13MB)
• Linux Binary: tagster_linux.zip (http://www.niehs.nih.gov/research/resources/software/tagster/docs/tagster_linux.zip)   (17MB)
• Software Manual: tagster_manual.pdf (http://www.niehs.nih.gov/research/resources/software/tagster/docs/tagster_manual.pdf)   (111KB)
• Detailed Algorithms: tagster_algorithm.pdf (http://www.niehs.nih.gov/research/resources/software/tagster/docs/tagster_algorithm.pdf)   (49KB)
• Evaluation Results: tagster_evaluation.pdf (http://www.niehs.nih.gov/research/resources/software/tagster/docs/tagster_evaluation.pdf)   (74KB)
• Tagster Tutorial: tagster_tutorial.pdf (http://www.niehs.nih.gov/research/resources/software/tagster/docs/tagster_tutorial.pdf)   (39K)
• Source code: please contact Jack Taylor

Credits

The TAGster was developed in and is maintained at the NIEHS by Zongli Xu, Norman L. Kaplan and Jack A Taylor.

Reference

Xu Z, Kaplan NL, Taylor JA. TAGster: efficient selection of LD tag SNPs in single or multiple populations. Bioinformatics. 2007 23:3254-5. Epub 2007 Sep 7.

Installation

The TAGster is written in Perl (http://www.perl.com/) and R (http://cran.us.r-project.org/) programming language, It can be run on Linux, or Microsoft Windows operating system with R (http://cran.us.r-project.org/) installed.

 Back to top