I did imputation with Hapmap and I have my dosage files. But the thing is I overlapped samples with different batches for running imputation (for e.g. 1 through 200 –one batch for imputation, then 150-300 next batch of imputation). Iam stuck as to how do I merge these into one file for association testing. I tried to find a way in plink but failed.
Please let me know if you are experienced with a way of doing it.