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.
- Does what I did look correct?
- How do I check the vcf file for accuracy?
Thank you in advance ,