I have converted a Ukbiobank bgen file to vcf for processing against a reference panel using beagle.
to make the pgen file from bgen I used the following.
plink2 --bgen ukb_imp_chr17_v3.bgen --sample ukb####_imp_chr17_v3_s#####.sample --make-pgen --keep-allele-order
There is a message that --keep-allele-order has no effect ..
This is the step for the vcf:
plink2 --pgen plink2.pgen --pvar plink2.pvar --psam plink2.psam --export vcf-4.2 vcf-dosage=DS bgz --from-bp 50 --to-bp 10000 --chr 17
The issue I see between the vcf I create and the reference panel is that at each location the Ref and Alt are opposite. This causes Beagle to fail and state there are no matches. Which is correct.
How can I switch or maintain the order of the Ref & Alt so beagle will match them?