How to build an imputation reference panel from a fasta file of many samples

Question

[moxu]

I have a fasta file for dozens of thousands of human mitochondrial genome sequences (aligned already) in fasta format. I want to construct a reference panel using these samples to impute genotyped samples, but I don't know how to do so properly.

BTW, anyone has thought about how to impute mtDNA markers? Someone tricked impute2 to take mtDNA as sex chromosome and then did the imputation. Not sure if there are other ways.

Thanks for any suggestions.