The primary publication for LAVA is:

Werme, J., van der Sluis, S., Posthuma, D. et al. An integrated framework for local genetic correlation analysis. Nat Genet 54, 274–282 (2022). https://doi.org/10.1038/s41588-022-01017-y (link)

When using LAVA, please refer to this paper.

The current R-implementation for LAVA, as well as documentation and tutorial, can be found in the GitHub repository here.

For questions, comments, feedback and feature requests, contact Christiaan de Leeuw or Josefin Werme.

Auxiliary files

The genome partition file used for the primary LAVA publication can be found in the support_data folder on the GitHub repository linked above, and the code used to create the partitioning can be found here. This partioning was created using the 1,000 Genomes phase 3 reference data (European panel, build GRCh37/hg19).

Custom binary LAVA LD reference files for European ancestry analyses as well as 1,000 Genomes phase 3 reference data in PLINK format for different ancestries can be found at the GitHub repository as well. Note that when analysing data from a non-European ancestry, a new genome partitioning will need to be created based on the reference data for that ancestry using the code linked above.