text: user3536: 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.
  
  user3694: I would also add that splitting your data into chromosomes allows you to run each chromosome in parallel (presuming you have some kind of server you can send each run to), vastly reducing the amount of time your analysis is going to take. I've not run all 22 chromosomes at once, but I can imagine it will take an enormous amount of time if you are using even a small number of markers and references.
  
  user3536: 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
  
original_text: 3536: <p>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.</p>
   3694: <p>I would also add that splitting your data into chromosomes allows you to run each chromosome in parallel (presuming you have some kind of server you can send each run to), vastly reducing the amount of time your analysis is going to take. I've not run all 22 chromosomes at once, but I can imagine it will take an enormous amount of time if you are using even a small number of markers and references.</p>
   3536: <p>OK, I ended up contacting one of the authors of the program, who kindly answered to my question:</p>
  
  <blockquote>
    <p>Either approach should work,</p>
  </blockquote>
  
  <p>[i.e. running the analysis by chromosome vs joining the data together]</p>
  
  <blockquote>
    <p>but I suggest dividing by chromosome because that approach has had
    more testing.</p>
  </blockquote>
  
  <p>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.</p>
  
  <p>Best,</p>
  
  <p>Max</p>
  