convert bgen to vcf in plink2.0

[CUMC]

Hi all,

I want to convert a bgen file to raw phased vcf in plink2., I used

plink2 --bgen ukb_imp_chr21_v3.bgen --sample ukb_imp_chr21_v3_s.sample --export vcf vcf-dosage=DS

but I got error message 

Error: --bgen now requires a REF/ALT mode ('ref-first', 'ref-last', or

'ref-unknown').  As of this writing, raw UK Biobank files are ref-first, while

older and PLINK-exported BGEN files are more likely to be ref-last.

Does anyone can help this out? Thank you sincerely!

Bill

[Yarden Hochenberg]

I am having the same problem. How did you handle this?

ב-יום רביעי, 14 ביולי 2021 בשעה 03:06:09 UTC+3, CUMC כתב/ה:

[Christopher Chang]

Have you tried reading the --bgen documentation?  ("plink2 --help bgen" gives you a short form of this.)