Supplemental datasets for GeneticsMakie.jl — ancestry LD reference panels

This datasets contains the LD reference panels for the following ancestry groups that can be used for the <code>GeneticsMakie.jl</code> (doi: https://doi.org/10.1101/2022.04.18.488573). The folder also contains the scripts that demonstrates the process of preparing the LD panels from the downloading step. The original LD panels were downloaded from the 1000 genomes project (Phase3, GRCh37) website. The ancestry notation is as follow: AFR: African AMR: American EAS: East Asian EUR: European SAS: South Asian Short descriptions of the scripts and the logs directory <code>1.download_and_prep_1kg_ld_panels.sh</code>: downloads and removes unnecessary SNPs (e.g. duplicated SNPs, SNPs have long indels) <code>2.filter_ld_panels_for_each_ancestry.ipynb</code>: prepares LD reference panels for each ancestry group with maf &gt; 0.05 and mac &gt; 1 using <code>Julia</code> <code>3.optional_sort_files.sh</code>: optionally, this script sorts the files by ancestry groups <code>logs</code> directory: for each chromosome, the log file shows the number of samples and SNPs before and after the process for each ancestry group本数据集包含适用于<code>GeneticsMakie.jl</code>（doi：https://doi.org/10.1101/2022.04.18.488573）的以下祖先群体的连锁不平衡（Linkage Disequilibrium，LD）参考面板。本文件夹同时包含演示从下载环节开始制备LD参考面板流程的脚本文件。原始LD参考面板下载自千人基因组计划（1000 Genomes Project，Phase3，GRCh37）官方网站。 祖先群体的命名规则如下：AFR：非洲裔（African）、AMR：美洲裔（American）、EAS：东亚裔（East Asian）、EUR：欧洲裔（European）、SAS：南亚裔（South Asian）。 以下为各脚本及日志目录的简要说明： <code>1.download_and_prep_1kg_ld_panels.sh</code>：用于下载并剔除冗余单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点（例如重复SNP、存在长插入缺失（insertion-deletion，indel）的SNP）。 <code>2.filter_ld_panels_for_each_ancestry.ipynb</code>：使用<code>Julia</code>语言为每个祖先群体制备符合最小等位基因频率（Minor Allele Frequency，MAF）>0.05且最小等位基因计数（Minor Allele Count，MAC）>1的LD参考面板。 <code>3.optional_sort_files.sh</code>：可选脚本，用于按照祖先群体对文件进行排序。 <code>logs</code>目录：针对每条染色体，日志文件会记录每个祖先群体在流程前后的样本数与SNP位点数量。