Dear all,

I'm trying to investigate how Beagle works when phasing with a reference panel and without a reference panel. I've got phased data of unrelated individuals that contain missing markers from these two commands (I'm using Beagle 3.3):

1) The first one goes with a reference panel.

java -Xmx444m -jar beagle.jar markers=./hapmap.markers phased=./hapmap.phased.bgl unphased=./hapmap.unphased.bgl missing=? out=./output

Phased data:

M rs12133813 G A G G

M rs7529536 G G G G

M rs3820577 G G G A

2) The second one goes without a reference panel.

java -Xmx444m -jar beagle.jar markers=./hapmap.markers unphased=./hapmap.unphased.bgl missing=? out=./output

Phased data:

M rs12133813 A G G G

M rs7529536 G G G G

M rs3820577 G G A G

I would like to ask you all what makes the results of two experiments different? Please give me some suggestions.

Thank you.