Tagger: Selection and evaluation of tag SNPs

Tagger is a tool for the selection and evaluation of tag SNPs from genotype data such as that from the International HapMap Project. It combines the simplicity of pairwise tagging methods with the efficiency benefits of multimarker haplotype approaches.

As input, users can upload genotype data in raw HapMap format or standard "pedigree" linkage format from which linkage disequilibrium patterns will be calculated. Alternatively, users can specify chromosomal landmarks to indicate genomic regions of interest within which tag SNPs are to be picked (a local copy of HapMap data will be used). This feature will be particularly useful for multiplex tag SNP design in multiple candidate genes. As output, Tagger produces a list of tag SNPs and corresponding statistical tests to capture all variants of interest, and a summary coverage report of the selected tag SNPs.

Tagger is developed by Paul de Bakker in the labs of David Altshuler and Mark Daly at the Center for Human Genetic Research of Massachusetts General Hospital and Harvard Medical School, and the Broad Institute. Tagger is described in "Efficiency and power in genetic association studies", Nature Genetics, 23 October 2005, and was used for analyses presented in "A haplotype map of the human genome", Nature, 27 October 2005.

Thanks to Itsik Pe'er, Stephen Schaffner, Nick Patterson, Roman Yelensky, Yves Chretien, Robert Graham, Maria Sun, Steven Wiltshire for help and suggestions.

Tagger has also been implemented in the stand-alone program Haploview by Julian Maller, David Bender and Jeffrey Barrett.

Links

Reference

P.I.W. de Bakker, R. Yelensky, I. Pe'er, S.B. Gabriel, M.J. Daly, D. Altshuler (2005) Efficiency and power in genetic association studies. Nature Genetics. 37: 1217-1223

Any questions?

You can contact us at tagger@broad.mit.edu.