Download LD Reference

Linkage-Disequilibrium (LD) matrices, which record pairwise correlations between genetic variants, are required as input to the VIPRS model. To facilitate running the model on GWAS data from diverse ancestries, we computed LD matrices for 6 continental populations represented in the UK Biobank. The six ancestry groups and their corresponding download links are listed below:

Code	Ancestry group	Sample size	Download
EUR	European	362446	GitHub or Zenodo
CSA	Central/South Asian	8284	GitHub or Zenodo
AFR	African	6255	GitHub or Zenodo
EAS	East Asian	2700	GitHub or Zenodo
MID	Middle Eastern	1567	GitHub or Zenodo
AMR	Admixed American	987	GitHub or Zenodo

The sample sizes here are restricted to unrelated individuals in the UK Biobank.

The matrices were computed using the block LD estimator, where we only record pairwise correlations between variants in the same LD block. The LD blocks are defined by LDetect. The matrices were computed using the sister package magenpy and were then quantized to int8 data type for enhanced compressibility.

For European samples, we also provide LD matrices that record pairwise correlations for up to 18 million variants. This matrix is available for download via Zenodo.

For more details on QC criteria, data preparation, etc., please consult our manuscript:

Zabad et al. (2025). Towards whole-genome inference of polygenic scores with fast and memory-efficient algorithms. BioRxiv.

To access and use these matrices for downstream tasks, consult the codebase of magenpy, our sister python package that implements specialized data structures for computing and processing large-scale LD matrices.

Bash Script for downloading/extracting LD matrices

Here is a bash script that can be used to download and extract the LD matrices for all 6 populations. The script uses the GitHub links provided above. Feel free to modify the script to suit your needs.

#!/bin/bash
output_dir="LD_matrices"
populations=("EUR" "CSA" "AFR" "EAS" "MID" "AMR")
extract=true

mkdir -p $output_dir

for pop in "${populations[@]}"
do
    echo "Downloading LD matrix for $pop"
    wget -O $output_dir/$pop.tar.gz "https://github.com/shz9/viprs/releases/download/v0.1.2/$pop.tar.gz"
    if [ "$extract" = true ]; then
        mkdir -p $output_dir/$pop
        tar -xf $output_dir/$pop.tar.gz -C $output_dir/$pop
    fi
done