Question: Strands are reversed
gravatar for richyanicky
19 months ago by
richyanicky10 wrote:


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?



beagle plink • 428 views
ADD COMMENTlink modified 19 months ago by GenoMax95k • written 19 months ago by richyanicky10

Use the 'ref-first' --bgen modifier.

"plink2 --bgen <bgen filename> ref-first --sample ..."

ADD REPLYlink written 19 months ago by chrchang5237.6k

That cleared up the issue Thank You!

ADD REPLYlink written 19 months ago by richyanicky10
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