[galaxy-user] Finding SNP differences between datasets

Hi, I am trying to find SNPs and/or indel variants that differ between two groups of samples. The data are 454 sequence capture results spanning a region of interest for a non-model organism without a complete genome. I have mapped these to my reference sequence of the region and generated BAM and pileup files for them. Does anyone know of a tool or method (either in galaxy or elsewhere) that will allow me to compare datasets and pick out variation between them (as opposed to things that differ from the reference sequence). Many thanks, Nicola