Using Beagle 4.1 for phasing and IBD - chromosomes I am trying to use beagle 4.1 for phasing and IBD analyses. I was wondering if I need to run the analysis by chromosome or I can put them together in the same vcf file.
OK, I ended up contacting one of the authors of the program, who kindly answered to my question:


  Either approach should work,


[i.e. running the analysis by chromosome vs joining the data together]


  but I suggest dividing by chromosome because that approach has had
  more testing.


I hope this might help other users, I saw that several questions regarding Beagle went unanswered on biostars and seqanswers. I guess it is a pretty specialized topic.

Best,

Max