Imputation and SNPs pipeline

Question

[dzisis1986]

Hello, I have an example.txt tab-separated file containing genotyping information of an individual and i would like to create a pipeline to analyze it in order to find Imputation (how many new SNPs can be confidently obtained through imputation) and SNP effects (genetic markers can be associated to conditions like vitamins). Do you know any available pipeline in R or a step-by-step pipeline to do this?

Here is an example of the data :

# rsid  chromosome      position        genotype
rs3094315       1       742429  AG
rs12562034      1       758311  AA
rs3934834       1       995669  AG
rs9442372       1       1008567 GG
rs3737728       1       1011278 GA
rs11260588      1       1011521 AA
rs6687776       1       1020428 TT
rs9651273       1       1021403 CC
rs4970405       1       1038818 AG

[4galaxy77]

Are you saying you want to impute variants in your file? That's not really done in R - but if you convert it to the right format, you can use the Sanger / Michigan imputation servers to impute your data.

[dzisis1986]

Not necessary in R ! I want to find imputation. I have never done it again so any tool or step- by step process of manipulating the data.