Reference panels

The eigenvalues and eigenvectors of LD matrices are essential input of HDL. For the European-ancestry population, we have computed these from 336,000 Genomic British individuals in UK Biobank. You can download these pre-computed reference files from the links in this instruction. We provided two sets of reference panel. The details can be found below.

1,029,876 QCed UK Biobank imputed HapMap3 SNPs

The size is about 32 GB after extraction. Although it takes more time, using the imputed panel provides more accurate estimates of genetic correlations. Therefore if your GWAS includes most of the HapMap3 SNPs, we recommend the usage of the imputed reference panel. You can download it here. Because the file size is large, in case of unstable internet connection, it is much more reliable to download the file using wget:

wget.exe -c -t 1 \
https://www.dropbox.com/s/trhbeg8vvx0zhdx/UKB_imputed_SVD_eigen99_extraction.tar.gz?dl=0 \
--no-check-certificate -O /Your/path/UKB_imputed_SVD_eigen99_extraction.tar.gz

If the downloading interrupts or gets stuck for a while, you can rerun the above command to continue downloading. When the file has finished downloading, you can check its MD5 hash to make sure the downloaded file is complete. For different operating system, this can be done by

md5sum /Your/path/UKB_imputed_SVD_eigen99_extraction.tar.gz  #Linux
md5 /Your/path/UKB_imputed_SVD_eigen99_extraction.tar.gz  #Mac
CertUtil -hashfile \Your\path\UKB_imputed_SVD_eigen99_extraction.tar.gz MD5  #Windows

The computation of MD5 may take a few minutes. If the MD5 hash is f8630c5ea678967b639b01c2e2b61934, then the downloaded file is complete. The extraction can be done by

cd /Your/path/
tar -xzvf UKB_imputed_SVD_eigen99_extraction.tar.gz

After successfully extracting all the files, the original .tar.gz file can be removed. If you prefer to download single files instead of the whole compressed file, you can find them here.

307,519 QCed UK Biobank Axiom Array SNPs

The size is about 7.5 GB after extraction. You can download it here or use wget by

wget.exe -c -t 1 \
https://www.dropbox.com/s/dswg8bu7hlrtqdl/UKB_array_SVD_eigen90_extraction.tar.gz?dl=0 \
--no-check-certificate -O /Your/path/UKB_array_SVD_eigen90_extraction.tar.gz

The MD5 hash should be 50722990fad9f84dff9ab66e65b58dd8. After successfully downloading and extraction, you may remove the compressed file.