I am working on file handling for GWAS. When I converted bgen to VCF by using plink2 with a commands below, all INFO (and also FILTER) columns became "." in the output VCF files. A column named IMP which correspond to imputed or not was disappear.
plink2 --bgen ref-first file.bgen --sample file.sample --keep id_list.txt --export vcf-4.2 bgz --out out
How can I keep INFO and some other informative columns when I convert bgen to VCF by using plink2?