Keeping indels, projecting reference coordinates?

[LovellHAGSC]

Hi there,
Is there any planned (or implemented) was to analyze indels via snp-sites? Basically, I want to annotate all variants (not just snps) in my multiple-sequence alignment and project those variants against the original reference (which also has indels) coordinate system.

Thanks,
John

[OwenDonohoe]

a response here would be appreciated