Create new Reference by merging SNV list with reference genome

[rdoan]

Hello,

I would like to create incorporate a list of 5 million single base variants (SNVs) into an existing reference sequence resulting in a new reference that would match my genome of interest. Alternatively, I could focus on coding regions and incorporate my SNV list into the mRNA of annotated genes.

Does anyone know of a good method to complete either of these?

Thanks