Consensus sequence

I have a use case that I am not sure the best way to proceed.

I have a non-model organism for which we would like to know the sequence
for a set of genes. It's a bird species, and I can for example align to the
zebra finch genome, then run bam_tally over a region to get  variants where
my species differs from zebra finch, and then infer the sequence based on
the reference and the variants.

But that seems harder than it should be. Is there some function that I am
missing that I can feed a GRanges and get back the consensus sequence for
that region, based on say a simple vote of the reads that overlap it?

Thanks,

Jim

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