[galaxy-user] Workflow assistance

After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following: I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed Bowtie alignments. I want to find the allelic positions where the (+) genomes differ from the (-) genome. Many thanks, Kevin