REFERENCE.md

In josefin-werme/lava: Local Analysis of [co]Variant Association

Preprocessed reference data

UK Biobank reference in LAVA binary LD format, version 1.1 (requires LAVA v0.1.5 or up)

Recommended for European ancestry analyses. LD is computed from 100,000 unrelated individuals of European ancestry from the UK Biobank, up to a distance of 10 megabases for each SNP. Total filesize is 15 Gb (unzipped), stored per chromosome. Note that the LAVA binary LD file format is unrelated to the LDSTORE .bcor file format.

Download links: - Chromosomes 1, 2 - Chromosomes 3, 4 - Chromosomes 5, 6 - Chromosomes 7 - 9 - Chromosomes 10 - 12 - Chromosomes 13 - 16 - Chromosomes 17 - 22 and X

List of wget commands for command line users:

wget https://vu.data.surfsara.nl/index.php/s/7NBVIvtPRdu7Qhz/download -O lava-ukb-v1.1_chr1-2.zip
wget https://vu.data.surfsara.nl/index.php/s/fy6ITboMojHrQXr/download -O lava-ukb-v1.1_chr3-4.zip
wget https://vu.data.surfsara.nl/index.php/s/mRz31q0lq7KMcuI/download -O lava-ukb-v1.1_chr5-6.zip
wget https://vu.data.surfsara.nl/index.php/s/89RXxPN2BlOqxLs/download -O lava-ukb-v1.1_chr7-9.zip
wget https://vu.data.surfsara.nl/index.php/s/3dU1L2Hap43xuCs/download -O lava-ukb-v1.1_chr10-12.zip
wget https://vu.data.surfsara.nl/index.php/s/DQqJ2Sqr49RP4xe/download -O lava-ukb-v1.1_chr13-16.zip
wget https://vu.data.surfsara.nl/index.php/s/U8eg5XfTr8qPzPp/download -O lava-ukb-v1.1_chr17-23.zip

1,000 Genomes reference genotype data in PLINK format

Data is obtained from 1000 genomes, and has been cleaned and preprocessed, split by ancestry. Note that as the sample size of the 1,000 Genomes cohorts is relatively small, larger genotype data sets of the same ancestry should be preferred if available.

Download links: - European - African - East Asian - South Asian - Middle/South American

josefin-werme/lava documentation built on July 17, 2025, 5:21 a.m.