Modern genetics studies require the use of many specialty software programs for various aspects of the statistical analysis. PHASE is a program often used to reconstruct haplotypes from genotype data, and Haploview is a program often used to visualize and analyze single nucleotide polymorphism data. Three new commands are described for performing these three steps: 1) exporting genotype data stored in Stata to PHASE, 2) importing the resulting inferred haplotypes back into Stata, and 3) exporting the haplotype/single nucleotide polymorphism data from Stata to Haploview.
AkeyJ., JinL., and XiongM.2001. Haplotypes vs single marker linkage disequilibrium tests: What do we gain?European Journal of Human Genetics9: 291–300.
2.
BarrettJ. C., FryB., MallerJ., and DalyM. J.2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics21: 263–265.
3.
CordellH. J., and ClaytonD. G.2005. Genetic association studies. Lancet366: 1121–1131.
4.
DevlinB., and RischN.1995. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics29: 311–322.
5.
GabrielS. B., SchaffnerS. F., NguyenH., MooreJ. M., RoyJ., BlumenstielB., HigginsJ., DeFeliceM., LochnerA., FaggartM., Liu-CorderoS. N., RotimiC., AdeyemoA., CooperR., WardR., LanderE. S., DalyM. J., and AltshulerD.2002. The structure of haplotype blocks in the human genome. Science296: 2225–2229.
6.
GoldsteinD. B.2001. Islands of linkage disequilibrium. Nature Genetics29: 109–111.
7.
MarchenkoY. V., CarrollR. J., LinD. Y., AmosC. I., and GutierrezR. G.2008. Semiparametric analysis of case–control genetic data in the presence of environmental factors. Stata Journal8: 305–333.
8.
MarchiniJ., CutlerD., PattersonN., StephensM., EskinE., HalperinE., LinS., QinZ. S., MunroH. M., AbecasisG. R., DonnellyP. and The International HapMap Consortium. 2006. A comparison of phasing algorithms for trios and unrelated individuals. American Journal of Human Genetics78: 437–450.
StephensM., and DonnellyP.2003. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics73: 1162–1169.
11.
StephensM., SmithN. J., and DonnellyP.2001. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics68: 978–989.
12.
The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature437: 1299–1320.
13.
ZhangK., QinZ. S., LiuJ. S., ChenT., WatermanM. S., and SunF.2004. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Research14: 908–916.
