Stata commands for moving data between PHASE and HaploView

Abstract 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 and Scheet 2005; Stephens, Smith, and Donnelly 2001) and one of the most popular programs for examining characteristics of the resulting haplotypes is HaploView (Barrett, et al. 2005). I will present 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 for further exploration.