Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

FST estimation

KE Kevin K. Esoh
TA Tobias O. Apinjoh
SN Steven G. Nyanjom
AW Ambroise Wonkam
EC Emile R. Chimusa
LA Lucas Amenga-Etego
AA Alfred Amambua-Ngwa
EA Eric A. Achidi
request Request a Protocol
ask Ask a question
Favorite

Prior to FST and PCA analyses, we LD-pruned the SNPs such that pairs with r2 > 0.1 within a window of 5 kb were pruned out using a step size of 50 bp. In addition, we excluded SNPs with MAF < 0.05. Pairwise FST estimates among the three ethnic groups within our study populations and among our study populations and the 1KGP3 reference populations were computed using smartpca. The tool computes the Hudson estimator of Wright’s FST which is immune to sample size differences, and uses a jackknife approach for ‘bootstrapping’, estimating a standard error and a Z score for the FST measurements. Regions of the genome with long-range LD listed in Table ​Table11 of Price et al.,86 were excluded from FST analysis and we further utilized smartpca’s LD regression function to correct for remnants of LD prior to FST estimation.

Copyright and License information: The Author(s) ©2021
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A