Question: How to just use 1000 genomes phase 3 CHB+JPT+CHS data as reference to impute?
0
gravatar for lovehopex
4.9 years ago by
lovehopex0
Taiwan
lovehopex0 wrote:

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. 

 

 

1000 genomes snp genotype impute2 • 1.8k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by lovehopex0
1

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 impuation accuracy.

See this and that overview.

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Jimbou750
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