How to just use 1000 genomes phase 3 CHB+JPT+CHS data as reference to impute?
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.
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lovehopex •
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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_happarameter when you get low imputation accuracy.See this and that overview.