bed format in step2 ( wgs data)

[quinnemma]

Hi,
I would like to try and use this pipeline with some wgs data - I can see from some previous comments that the only way to do this is to convert to bed format using plink2.
REGENIE itself will allow bed input for step2 but I can't see an option to do this using this pipeline as it only accepts bgen for step2(genotypes_association_format) or did I miss something?

thanks for your help!
Emma