Tools in the Samtools and Picard groups can filter BAM/SAM datasets, but the best you will be able to do is isolate proper mapped pairs with these methods. Once that is done, you could manipulate the data further with tools in Text Manipulation & Filter and Sort, to look for identifiers that appear only once.
You are likely to miss many good/valid hits with this way of filtering, but I suppose that you know that already.
Increasing the map criteria is also another way to filter, but reads that multi-map with high quality will also result.
Good luck, Jen, Galaxy team