Phasing vcf file with Beagle

0

Hello all,

I tried to phase my vcf files with Beagle. All the genotypes seem to be phased but the INFO field containing annotations of interest disappeared and I want to keep it. How can I do that ? In case it's not possible to keep the INFO field with Beagle, is there a way to fuse my new phased vcf file with the old one in order to add the INFO field ?

Here's the command line I used:
java -Xmx2g -jar /home/Softs/beagle/beagle.27Apr20.b81.jar gt=out.vcf out=phased_beagle

Also, I didn't specify a reference panel or a map. Is it necessary and why ? I don't find their manuals/instructions clear enough.

Thank you for your help!


vcf


phasing


beagle


haplotype


bash

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