Genotype imputation using BEAGLE 3.3.2
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7.5 years ago


I have a few questions regarding genotype imputation using Beagle.

I am very new in the bioninformatics field, so forgive me if I am asking any dumb questions.

  1. Can anyone post here an example of a genotype imputation command line? I don't know if I am doing it right.
  2. Regarding the markers file. I am using SVS to prepare my data.

    a. Do I necessarily need to apply a markers map to my data before exporting it to beagle?

    b. how do I create a markers file for beagle?

I have two files: one with genotype data for a group of sires (30 individuals) genotyped using a 770K markers chip, and another one with the offspring for those sires (around 804) genotyped using a 50K markers chip

The sires will be used to impute the offspring

So, I need to have in my markers file only the list of markers used to gneotype the sires. How do I filter this data and how do I create this marker file?

If you can explain me using a very simple language and give me examples of commands I should be using that would be very helpful.

I am very new in the field and am pretty lost!

Thank you in advance

Beagle genotype-imputation • 3.5k views
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Hi I'm sorry but I need to know if you found answers to your question, because I have the same issue, I don't know how can I introduce the information to the Beagle program.

Entering edit mode

HI, I actually have. What do you need to know exactly?

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Hi, thanks for writing

Well my question is if you know which format I need to use when I'm trying to make an imputation if I have 6k to 50k, because when I'm did this I don't receive the result I'm looking for.

When I put my format of 6k to 50k, beagle not fill the missing fields, so I think I'm wrong in some field that I used.

Can you help me with this situation? because I'm feeling lost.

Thanks so much for your help.


Entering edit mode

Hello, I have a new question. In the marker file its correct that I use the? Or that cant be because when I ran the software an error appears? So I don't know how that I need to introduce the information. I think I have an error with my markers file. Or genotype file or maybe in the refer panel. Where can I contact you? Because if you have time I appreciate your help thanks. My email is thanks


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