mkanai/finemapping-pipeline

finemapping-pipeline's Issues

In-sample LD matrix for GTEx?

Hi @mkanai

Thanks for your amazing work Insights from complex trait fine-mapping across diverse populations. I have a simple question regarding this work, because I couldn't find the other accompanying paper (An annotated atlas of causal variants for complex human traits).
My question is about the colocalization approach you used, especially:

We assembled fine-mapping results of cis-eQTL associations from GTEx47 v8 (detailed in our accompanying paper8) and eQTL catalogue48 release 4, both of which used the same or the functionally-equivalent fine-mapping pipelines to our GWAS fine-mapping

Since SuSiE needs LD matrx (in-sample) for eQTL data, may I ask are these LD matrices publicly available (e.g. in npz or BCOR or other formats)?

Thanks!
Oveis

Documentation/example data use case

Hey, your repository looks like it is exactly what I need and I would love to use it. However, there doesn't seem to be any documentation on how to run it or an example dataset use case? Is this something you could add or point me towards (or even list the steps here to running it)?

Thanks,
Alan.