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

Zicheng Zhao; Yinan Wang; Zhe Zhang; Shuai Cheng Li

doi:10.1016/j.xpro.2022.101928

Author(s)

Zicheng Zhao
Yinan Wang
Zhe Zhang
Shuai Cheng Li

Related Research Unit(s)

Department of Computer Science

Detail(s)

Original language	English
Article number	101928
Journal / Publication	STAR Protocols
Volume	4
Issue number	1
Online published	13 Dec 2022
Publication status	Published - 17 Mar 2023

Link(s)

DOI	DOI https://doi.org/10.1016/j.xpro.2022.101928 Final Published version
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Attachment(s)	Documents 129836202.pdf Final Published version, 2.5 MB, PDF Publisher's Copyright Statement This full text is made available under CC-BY-NC-ND 4.0. https://creativecommons.org/licenses/by-nc-nd/4.0/
Link to Scopus	https://www.scopus.com/record/display.uri?eid=2-s2.0-85144081785&origin=recordpage
Permanent Link	https://scholars.cityu.edu.hk/en/publications/publication(6a6ad78a-e7e3-4590-8921-ae75c3d26a68).html

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.