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 GeneticsMakie.jl (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

1.download_and_prep_1kg_ld_panels.sh: downloads and removes unnecessary SNPs (e.g. duplicated SNPs, SNPs have long indels)

2.filter_ld_panels_for_each_ancestry.ipynb: prepares LD reference panels for each ancestry group with maf > 0.05 and mac > 1 using Julia

3.optional_sort_files.sh: optionally, this script sorts the files by ancestry groups

logs directory: for each chromosome, the log file shows the number of samples and SNPs before and after the process for each ancestry group