GENHW: Hardy-Weinberg equilibrium test and allele frequency estimation

Description: genhw estimates allele, genotype frequencies and disequilibrium coefficients, and performs asymptotic Hardy-Weinberg (HW) equilibrium tests. In the case of biallelic markers it also computes an exact HW significance probability.

genhw expects the data to be in long format. That is, each observation  contains the two allele values at the locus being examined (all1 and all2). Allele values can be numeric or string.

genhwi is the immediate form of genhw using the genotypic counts on the command line; (i.e. genhwi #AA  #Aa  #aa ) where #AA, #Aa and #aa are the counts for the AA, Aa and aa genotypes. Note that this immediate command only works with biallelic loci.

If you use this program please reference:   Cleves MA.Hardy-Weinberg Equilibrium Tests and Allele Frequency Estimation. STATA Technical Bulletin. No. 48, March 1999, 34-37