Entering edit mode
5.6 years ago
gunnhelenmoen
•
0
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?
Can you show a few lines of the impute file ?
The impute dataset would look something like this:
each line would be followed by the the probabillity for the genototype for each individual
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 :)