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.

1000genomes genotype snp impute2

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updated 3.9 years ago by Ram 4.5K • | written 11.2 years ago by lovehopex 0

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.

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updated 3.9 years ago by Ram 4.5K • | written 11.2 years ago by Jimbou 96

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