I have a list of files from UKbiobank imputed data. And I wonder how can I merge 22 chromosome data. Each chromosome has their own data looks like below:
ukb_imp_chr1_v3.bgen ukb_imp_chr1_v3.bgen.bgi ukb41999_imp_chr1_v3_s487296.sample
I tried to use plink2 but I don't see options that can read bgen.bgi.
plink2 \ --bgen *imp*.bgen ref-first \ --sample *imp*.sample \ --pmerge-list list_bgen_imp.txt \ --make-pgen --out ukb_imp_allChrs
I thought the index file(bgi) is important but don't know how to involved in my code...