mPopTag

mPopTag: The Multi-Population Tag SNP Picker

The Multi-Population Tag Single Nucleotide Polymorphism (SNP) Picker (mPopTag) is a tool used to select or evaluate linkage disequilibrium (LD) tag SNPs for multiple populations. The program analyzes patterns of LD--measured by composite linkage disequilibrium (CLD) or r2--between polymorphic sites in a genome region for multiple populations. It also uses an agreedy algorithm to select a single set of near-minimum numbers of LD tag SNPs for multiple populations.

Downloads

• Linux Binary: mpoptag_linux.zip (http://www.niehs.nih.gov/research/resources/software/mpoptag/docs/mpoptag_linux.zip)   (4MB)
• Software Manual: manual.pdf (http://www.niehs.nih.gov/research/resources/software/mpoptag/docs/manual.pdf)   (31KB)
• Source code: please contact Jack Taylor

Credits

The mPopTag 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. Tag SNP selection for candidate gene association studies using HapMap and gene resequencing data. Eur J Hum Genet 2007 Oct;15(10):1063-70.

Installation

It can be run on Linux operating system.