<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>

CC BY-SA 4.0
2018-11-16T23:35:29.907Z
This would be better served as a comment to the answer since it does not stand as a answer itself
Bioathlete
CC BY-SA 4.0
2018-11-16T10:27:51.230Z
2018-11-16T10:27:51.230Z
user438383
<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>

CC BY-SA 4.0
2018-11-25T14:05:55.667Z
I don't see many questions about phasing and IBD detection on bioinformatcis SE. I think that's just because it's still a small site and there aren't that many people from that field on it yet. I wish there were more questions!
winni2k
CC BY-SA 4.0
2018-11-03T16:29:13.040Z
2018-11-03T16:29:13.040Z
Max_IT
<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>

CC BY-SA 4.0
2018-10-31T13:36:20.193Z
Well, I am new here, do you mind to give me some feedback on why the -1 on my question? Not trying to argue, just trying to improve.
Max_IT
CC BY-SA 4.0
2018-11-01T15:49:05.397Z
I'm not sure who downvoted your question, but maybe because you don't have any info about what you have done so far or what you aim to achieve? In any case I think the question and the answer you need are clear enough, so +1. If you find out the answer to your question by some other means we would be happy if you submit an answer to your question.
conchoecia
CC BY-SA 4.0
2018-11-03T16:23:00.857Z
Thank you for your explanation. I believe it should be clear enough for anyone familiar with the program. I ended up contacting one of the authors, I will post his answer here.
Max_IT
<snp><phasing>
Using Beagle 4.1 for phasing and IBD - chromosomes
# Using Beagle 4.1 for phasing and IBD - chromosomes

(Asked by: username_0 on 2018-10-30)

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.

**Tags:** snp, phasing
> **Comments:**
> **username_0**: Well, I am new here, do you mind to give me some feedback on why the -1 on my question? Not trying to argue, just trying to improve.  
> **username_1**: I'm not sure who downvoted your question, but maybe because you don't have any info about what you have done so far or what you aim to achieve? In any case I think the question and the answer you need are clear enough, so +1. If you find out the answer to your question by some other means we would be happy if you submit an answer to your question.  
> **username_0**: Thank you for your explanation. I believe it should be clear enough for anyone familiar with the program. I ended up contacting one of the authors, I will post his answer here.  

---

## 2 answers

### Answer by username_0 on 2018-11-03. Score: 4 | Accepted answer

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

> **Comments:**
> **username_4**: I don't see many questions about phasing and IBD detection on bioinformatcis SE. I think that's just because it's still a small site and there aren't that many people from that field on it yet. I wish there were more questions!  

---

### Answer by username_2 on 2018-11-16. Score: 1

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.

> **Comments:**
> **username_3**: This would be better served as a comment to the answer since it does not stand as a answer itself  

---

