Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations

Hou, K.; Gogarten, S.; Kim, J.; Hua, X.; Dias, J.-A.; Sun, Q.; Wang, Y.; Tan, T.; Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group,; Atkinson, E. G.; Martin, A.; Shortt, J.; Hirbo, J.; Li, Y.; Pasaniuc, B.; Zhang, H.

doi:10.1101/2023.09.30.560263

bioRxiv · 10.1101/2023.09.30.560263

Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations

Hou, K.·Gogarten, S.·Kim, J.·Hua, X.·Dias, J.-A.·Sun, Q.·Wang, Y.·Tan, T.·Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group,·Atkinson, E. G.·Martin, A.·Shortt, J.·Hirbo, J.·Li, Y.·Pasaniuc, B.·Zhang, H.

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Abstract

SummaryAdmixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic study of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations. Availability and implementationAdmix-kit package is open-source and available at https://github.com/KangchengHou/admix-kit. Additionally, users can use the pipeline designed for admixed genotype simulation available at https://github.com/UW-GAC/admix-kit_workflow.

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Hou, K., Gogarten, S., Kim, J., Hua, X., Dias, J.-A., Sun, Q., Wang, Y., Tan, T., Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group,, Atkinson, E. G., Martin, A., Shortt, J., Hirbo, J., Li, Y., Pasaniuc, B., Zhang, H.. 2023-10-02. Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations. https://doi.org/10.1101/2023.09.30.560263

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