Hi all, Since my last post has not been responsed, I want to post this question to make my question more understandable.
1) I downloaded the genotypes for HapMap individuals from the hapmap website, however, there are some missing genotypes for some SNPs among the individuals. I used IMPUTE2 to impute the genotypes based on 1000G panel. Should I obtain more SNPs that are in LD with the original SNPs from the imputation? I expected the results, but my results only have an additional 1K SNPs from the imputation? Why?
2) BIMBAM is also a widely used software package for imputation, however, it seems that it needs the phenotype of the individuals. For those individuals of GWAS, we can assign "0" and "1" for the samples as phenotype. Then how can I deal with the HapMap samples since they are all normal samples, should I assign "1" to all of them?
If anyone has the answer, could you please give me a hint?