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Protocol to analyze population structure and migration history based on human genome variation data
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.
STAR Protocols
|December 15, 2022
Summary
This protocol integrates human genome variation data to analyze population structure and migration. It uses scripts for variant filtering, principal component analysis, and ancestry analysis, aiding population genetics research.
Area of Science:
- Population Genetics
- Human Evolutionary Biology
- Bioinformatics
Background:
- Integrating diverse genome variation datasets is challenging.
- Understanding human population structure and migration requires robust analytical methods.
Purpose of the Study:
- To present a protocol for integrating genome variation data.
- To explore human population structure and migration history.
Main Methods:
- Semi-automated scripts for data integration and analysis.
- Variant filtering, principal component analysis, and ancestry component analysis.
- Inference of historical population size and migration patterns using SNPs, genotype likelihoods, and haplotypes.
Main Results:
- The protocol effectively visualizes the impact of variant filtering on batch effects.
- It enables detailed exploration of population structure and migration history.
- The methods are adaptable to various genome variation data sources.
Conclusions:
- The described protocol offers a comprehensive approach to analyzing human population genetics.
- It facilitates the integration and exploration of diverse genomic datasets.
- This method aids in understanding human evolutionary history and population dynamics.
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