Multi-allelic exact tests for Hardy-Weinberg equilibrium that account for gender

Abstract Statistical tests for Hardy–Weinberg equilibrium are important elementary tools in genetic data analysis. X‐chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing autosomal variants for equilibrium. Recently, we proposed specific X‐chromosomal exact test procedures for bi‐allelic variants that include the hemizygous males, as well as autosomal tests that consider gender. In this study, we present the extension of the previous work for variants with multiple alleles. A full enumeration algorithm is used for the exact calculations of tri‐allelic variants. For variants with many alternate alleles, we use a permutation test. Some empirical examples with data from the 1,000 genomes project are discussed.