The coloc package can be used to perform genetic colocalisation analysis of two potentially related phenotypes, to ask whether they share common genetic causal variant(s) in a given region.

Most of the questions I get relate to misunderstanding the assumptions behind coloc (dense genotypes across a single genomic region) and/or the data structures used. Please read vignette("a02_data",package="coloc") before starting an issue.

version 5

This update (version 5) supercedes previously published version 4 by introducing use of the SuSiE approach to deal with multiple causal variants rather than conditioning or masking. See

for the full SuSiE paper and

for a description of its use in coloc.

To install from R, do

   install.packages("remotes") # if necessary

Note that in all simulations, susie outperforms the earlier conditioning approach, so is recommended. However, it is also new code, so please consider the code “beta” and let me know of any issues that arise - they may be a bug on my part. If you want to use it, the function you want to look at is coloc.susie. It can take raw datasets, but the time consuming part is running SuSiE. coloc runs SuSiE and saves a little extra information using the runsusie function before running an adapted colocalisation on the results. So please look at the docs for runsusie too. I found a helpful recipe is 1. Run runsusie on dataset 1, storing the results 2. Run runsusie on dataset 2, storing the results 3. Run coloc.susie on the two outputs from above

More detail is available in the vignette a06_SuSiE.html accessible by


Background reading

For usage, please see the vignette at

Key previous references are:

Frequently Asked Questions

see FAQ

Notes to self

to generate website:

Rscript -e "pkgdown::build_site()"