Question: Exctracting genotype data on a single SNP from all individuals in a dataset
0
gravatar for gunnhelenmoen
5 days ago by
gunnhelenmoen0 wrote:

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 gene genome • 64 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by gunnhelenmoen0

Can you show a few lines of the impute file ?

ADD REPLYlink written 5 days ago by Inquisitive899530

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

ADD REPLYlink written 5 days ago by gunnhelenmoen0

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 :)

ADD REPLYlink modified 3 days ago • written 3 days ago by Inquisitive899530
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1873 users visited in the last hour