TUNA: Testing UNtyped Alleles

TUNA is a free software package for estimating allele frequencies for all the SNPs available in a population reference panel (e.g. HapMap database) based on genotype data from a subset of markers (e.g. the Illumina HumanHap300 BeadChip SNP set) in a group of subjects (e.g. the cases in a case-control sample).

Current release: version 1.1.2 beta (released in July, 2007)

Download: Please click here to register and download

Documentation: [PDF]

Sample input files: can be viewed and downloaded here

Questions and bug reports: should be addressed to wen at galton.uchicago.edu

References:
1.Nicolae DL (2006) "Quantifying the Amount of Missing Information in Genetic Association Studies". Genetic Epidemiology, 30(8):703-717. [link]

2.Nicolae DL (2006) "Testing untyped alleles (TUNA) - applications to genome-wide association studies". Genetic Epidemiology, 30(8): 718-727a. [link]

3.Wen X. and Nicolae DL (2007) "Case-control association studies of untyped markers with TUNA" Bioinformatics,doi:10.1093/bioinformatics/btm603. [link]