How to just use 1000 genomes phase 3 CHB+JPT+CHS data as reference to impute?

Question

[lovehopex]

I want to just use 1000 genomes phase 3 CHB+JPT+CHS data as reference to impute.

I wonder whether the option in IMPUTE2 program can help me do this.

Or how can I do this?

Thank you.

[Jimbou]

Did you try to run the imputation with standard options? Because impute2 decides on its own which haplotypes to use for imputation. You can play with the k_hap parameter when you get low imputation accuracy.

See this and that overview.