Hello, I imputed my data with TopMed imputation server, and now I have 3 problems
1- I have no more rs ID, all variants are chrXX:00000000 format. How can I resolve this, I am working on vcf and plink files
2- If I allply an r² threshold, could I keep the physically genotyped variants or it will keep only the best imputed as genotyped variants have no r² ?? 3- The results from genotyped data showed a strong association signal, but this signal disappeared with the imputed data. Could it an imputation error ??
Thank you very much