I'd love to be able to compare alignments (SAM/BAM; short reads) to two different reference sequences that are aligned to each other. The two (or more) reference sequences would be aligned to each other, to obtain a common frame (with gaps) that would then be used to adjust and display the short read alignments to each reference. For instance, if reference 2 has an insertion with respect to the reference 1, then a gap would be introduced in reference 1, and all reads aligned to reference 1, in order to be able to display both ref's and their short read alignments, all in a common frame.
This seems very do-able ... all one would need is the BAM files for each reference, then a multiple alignment of the references against each other, and the gapping / mismatch information from the multi-alignment would be used to adjust the display of the BAMs.
Does this, or something like this, exist?