how to perform GWAS on UKBiobank data?

Question

[anamaria]

Hello,

I am trying to access this software here: https://jmarchini.org/bgenie/

and to register for it in order to download it but it says that the form has been deactivated? Can this be download any other way?

If now do you have any recommendations which software to use to perform GWAS on UKBiobank data?

Say I would have BGEN files downloaded.

Thanks Ana

[GZ1995]

Plink2 supports BGEN files as input, which I guess is the most commonly used software to perform GWAS.

[Garan]

You might want to try BOLT-LMM https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309610/, it's what we currently use for our analysis of UK Biobank data. We're also looking at using SAIGE but don't have the run times for UK Biobank yet.