Exctracting genotype data on a single SNP from all individuals in a dataset
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2.5 years ago

I want to exstract a single SNP from my .impute file (created using IMPUTE2). I want this information as a plink file with genotype on all in individuals in the study at this particular posistion. When working with non-imputed data I've used this command line:

./plink --bfile GWASfile --snps rsXX --make-bed --out outputfile


This does however not work when I dont have the file in a plink format, but in a large .impute file.

Does anyone know how I can make this plink file from the impute file?

SNP genome gene • 869 views
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Can you show a few lines of the impute file ?

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The impute dataset would look something like this:

--- 22:16050075:A:G 16050075 A G
--- 22:16050115:G:A 16050115 G A
--- 22:16050213:C:T 16050213 C T
--- rs367963583:16050922:T:G 16050922 T G


each line would be followed by the the probabillity for the genototype for each individual

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Can you try and create a format similar to what 23andme uses? Like what is given below.

# rsid chromosome position genotype

rs3094315 1 742429 AG

rs12562034 1 758311 AG

rs3934834 1 995669 CC

Then you can use plink to change that file to a bed or ped file and proceed with your extraction. ( https://www.cog-genomics.org/plink/1.9/input#23file ). This is a suggestion not sure if that would work. Do Let me know if it does :)

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