I recently had to perform a genome-wide association study and performed genotype imputation to increase the number of SNPs I can evaluate.
For that I used the Michigan Imputation Server. I combined all the necessary preprocessing steps and optional filtering steps in an easy to use workflow and also show how you can use the API to circumvent using the web interface.
The workflow is nothing special, and primarily combines already existing scripts, but I think it might still be useful for people who are new to genotype imputation.
You can find the code on my github.
If you find it useful, feel free to star the repository.