How to run GWAS on imputed HLA alleles using Regenie

You can run association testing on imputed HLA alleles with REGENIE using the modifiable REGENIE DF12 pipeline, accessible through the Pipelines tool in the Sandbox.

Required changes to inputs

The workflow inputs contain a value "regenie.sub_step2.bgenlist", which determines which genotype information to use for running REGENIE, i.e. which variants to run the association analysis on. By changing this to the DF12 HLA allele data, "LIBRARY_RED/finngen_R12/hla_1.0/bgen/hla_chunks", the pipeline will run the association analysis on imputed HLA alleles.

Apart from that, proceed according to the instructions on how to run GWAS using REGENIE to prepare the required inputs.