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!