Hello

I have imputed data from ukbiobank in bgen format. I would like to convert it to a vcf file.

I can use plink2 to make pgen files and then use plink2 again to create a vcf

    plink2 --bgen ukb_imp_chr17_v3.bgen --sample ukimp_chr17_v3_s.sample --make-pgen

    plink2 --pgen plink2.pgen --pvar plink2.pvar --psam plink2.psam  --export vcf

This creates a vcf file but it doesn't seem to process in any of our pipelines. 

1. Does what I did look correct?
2. How do I check the vcf file for accuracy?

Thank you in advance ,

Richard
Assuming you want dosage information in your VCF, you need to replace "--export vcf" with something like "--export vcf vcf-dosage=DS".  You may also want to add the 'bgz' modifier to request bgzipping of the VCF file.