How to download BGEN files?

[Ana Marija]

Hello,

I want to use this software but in the data I downloaded from my project from UKBiobank I only have these files available.

> list.files()
 [1] "archive.tar.gz"                "encoding.ukb"                
 [3] "fields.ukb"                    "HESDataDic.xlsx"             
 [5] "HESTables.xlsx"                "HospitalEpisodeStatistics.pdf"
 [7] "k44316.key"                    "ukb31212.csv"                
 [9] "ukb31212.enc"                  "ukb31212.enc_ukb"            
[11] "ukb31212.html"                 "ukb31212.log"                
[13] "ukb31212.r"                    "ukb31212.tab"                
[15] "ukbconv"                       "ukbgene"                     
[17] "ukbmd5"                        "ukbunpack"

Do you know from where and how I can download corresponding BGEN files?

I am very new to this.

Thanks

Ana

[Milton Pividori]

Hi Ana,

Thank you for your interest in ukbREST. Looks like you already followed the process to convert your phenotype data to csv and html. That's the phenotype part of your data. To download the BGENs (genotypes), you should have received an email from UK Biobank with the instructions to download them (it's a different process).

I would send an email to them (acc...@ukbiobank.ac.uk) with this question.

Regards,

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Milton Pividori, PhD

Postdoctoral Scholar, Section of Genetic Medicine

The University of Chicago Medicine & Biological Sciences

5841 S. Maryland Ave., Suite N414, Chicago, IL 60637, USA

Chicago, IL 60637 USA

[Ana Marija]

Hi Milton,

isn't this the procedure on how to download genotypes

http://biobank.ctsu.ox.ac.uk/showcase/showcase/docs/ukbgene_instruct.html#aut

and if yes would I choose there imputation data, for example:

ukbgene imp -c17

Thanks

Ana

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