Supplemental datasets for GeneticsMakie.jl — ancestry LD reference panels

<p>This datasets&nbsp;contains the LD reference panels for the following ancestry groups&nbsp;that can be used for the&nbsp;<code>GeneticsMakie.jl</code>&nbsp;(<a href="https://www.biorxiv.org/content/10.1101/2022.04.18.488573v1">doi: https://doi.org/10.1101/2022.04.18.488573</a>). 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&nbsp;<a href="https://www.internationalgenome.org/">1000 genomes project (Phase3, GRCh37)</a>&nbsp;website.</p> <p>The ancestry notation is as follow:</p> <ul> <li>AFR: African</li> <li>AMR: American</li> <li>EAS: East Asian</li> <li>EUR: European</li> <li>SAS: South Asian</li> </ul> <p>Short descriptions of the scripts and the logs directory</p> <ul> <li><code>1.download_and_prep_1kg_ld_panels.sh</code>: downloads and removes unnecessary SNPs (e.g. duplicated SNPs, SNPs have long indels)</li> <li><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&nbsp;<code>Julia</code></li> <li><code>3.optional_sort_files.sh</code>: optionally, this script sorts the files by ancestry groups</li> <li><code>logs</code>&nbsp;directory: for each chromosome, the log file shows the number of samples and SNPs before and after the process for each ancestry group</li> </ul>