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Protocol to analyze population structure and migration history based on human genome variation data

We describe a protocol to integrate genome variation data from different datasets and explore the population structure and migration history of human populations. This protocol provides semi-automated scripts to perform and visualize the effect of variant filtering strategy on eliminating batch effe...

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Detalles Bibliográficos
Autores principales: Zhao, Zicheng, Wang, Yinan, Zhang, Zhe, Li, Shuai Cheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9758492/
https://www.ncbi.nlm.nih.gov/pubmed/36520631
http://dx.doi.org/10.1016/j.xpro.2022.101928
Descripción
Sumario:We describe a protocol to integrate genome variation data from different datasets and explore the population structure and migration history of human populations. This protocol provides semi-automated scripts to perform and visualize the effect of variant filtering strategy on eliminating batch effects, principal component analysis, ancestry component analysis, historical population effective size inference, and migration and isolation analysis based on independent biallelic SNPs, genotype likelihoods, and haplotypes. The protocol can be adapted to variation data from other sources. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).(1)