How to run GWAS on imputed HLA alleles using Regenie
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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.
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 to prepare the required inputs.