I want to use beagle to phase my genotyped per chromosome, my data is in AB, format. When I run using the java -Xmx1000m -jar beagle.jar unphased=fileA.bgl missing=? out=Myrun, I am not getting phase data per chromosomes and I am also expecting the program to show me running per chromosomes. Is there a specific command I should type together with the above command to achieve this, the other question is I don't have a reference panel. Where can I get the reference panel for Bovine if I were also to include it. Any help will be appreciated