Ref.-guided consensus using alt. alleles

[jmartin]

I've recently used samtools mpileup to generate a reference guided consensus sequence of my data. But the consensus includes IUPAC degenerate characters to represent sites of variation. What I'd like to do is to generate the same consensus, but reporting the 'alternate' allele (the allele from my data) at each of those sites.

Is there an easy way to do this already out there? I can see how I could script something up that would use the vcf to get this done, but I don't want to re-invent the wheel if something can already do this.