Exporting and importing Stata genotype data to and from PHASE and HaploView

Genetic association studies often explore the relationship between diseases and collections of contiguous genetic markers located on the same chromosome known as haplotypes. Haplotypes are usually not observed directly but are inferred statistically using a variety of algorithms. One of the most popular haplotype inference programs is PHASE (Stephens & Scheet, (2005). Accounting for decay of linkage disequilibrium in haplotype inference and missing data imputation. American Journal of Human Genetics, 76, 449-462.; Stephens, Smith, & Donnelly, (2001). "A New Statistical Method for Haplotype Reconstruction from Population Data", American Journal of Human Genetics, 68, 978-989) and one of the most popular programs for examining characteristics of the resulting haplotypes is HaploView (Barrett, Fry, Maller, & Daly (2005) "Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265). We have developed a set of Stata commands for exporting genotype data from Stata into PHASE, importing the resulting haplotypes back into Stata for association analysis and exporting the haplotype data from Stata into HaploView.