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

被引：2
作者：
Zhao, Zicheng [1 ,2 ]
Wang, Yinan [3 ,4 ]
Zhang, Zhe [5 ]
Li, Shuai Cheng [1 ]
机构：
[1] City Univ Hong Kong, Dept Comp Sci, Kowloon, Hong Kong 999077, Peoples R China
[2] Shenzhen Byoryn Technol Co Ltd, Shenzhen 518000, Peoples R China
[3] Peking Univ Shenzhen Hosp, 1120 Lianhua Rd, Shenzhen 518036, Peoples R China
[4] Southern Univ Sci & Technol, Sch Med, 1088 Xueyuan Ave, Shenzhen 518055, Peoples R China
[5] Jinan Univ, Zhuhai Peoples Hosp, Zhuhai Hosp, Dept Cardiol, 79 Kangning Rd, Zhuhai 519000, Peoples R China
来源：
STAR PROTOCOLS | 2023年 / 4卷 / 01期
关键词：
ASSOCIATION; DISCOVERY; FRAMEWORK; INFERENCE; ADMIXTURE; SNP;
D O I：
10.1016/j.xpro.2022.101928
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
We describe a protocol to integrate genome variation data from different data sets 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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页数：21
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