I am doing a process of genotypes imputation, however, still have questions:
if I understand correctlt, the imputation is used to fill those missing genotypes of some SNPs, applying the panel genotypes from HapMap and 1000G. However, when I came to the condition to compare the two GWAS genotypes, which were conducted under different array platform, i want to add some LD SNPs not in GWAS platform but in reference panel to the two genotypes files
I used impute2 to do such a thing using 1000G reference, it did add many SNPs into the genotypes, but lots of them can not pass the maf >0.05 & geno>0.9 threshold of plink. I looked into the files, and lots of the added SNPs do not have a rs#, is that correct?
So I guess i am doing the wrong job.
If you know the exact thing of this issue, could you give me some points?