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LAAA: Local Ancestry and Allelic Association

LAAA, the pipeline for Local Ancestry and Allelic Association, was developed to facilitate the local ancestry adjusted association analysis in admixed populations. The pipeline takes plink format genotype data as input, converts file format internally and performs local ancestry inference using HAPMIX. With the estiamted local ancestry, the pipeline goes through a novel two-step testing procedure developed by us. Our two step testing procedure takes into account the presence of local ancestry in admixed populations, thus achieving well-controlled type I error and enhanced power. In the first step, it robustly captures associations due to allele effect, ancestry effect and, particularly, the existence of effect heterogeneity between the two ancestral populations. In the second step, it accurately identifies the source of association. It is particularly powerful in detecting the presence of interaction between ancestry and allele effect.

The current version is a pre-release. For details, please refer to our tutorial. Comments and suggestions are welcome, please e-mail Qing Duan at or Yun Li at