Protocol to analyze population structure and migration history based on human genome variation data
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Updated: Aug 17, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Zicheng Zhao1, Yinan Wang2, Zhe Zhang3
1Department of Computer Science, City University of Hong Kong, Kowloon 999077, Hong Kong; Shenzhen Byoryn Technology Co., Ltd., Shenzhen 518000, China.
Abstract:
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.
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