Existing Tools For Post-Processing After Aligning Paired-End Reads With Blat?

Hi,

I'm wondering if there are existing tools that can do post-processing on paired-end reads' BLAT output.

More specifically, I'd like the tool to "merge" the alignments from the alignments of each pair's ends and remove the inconsistent alignments while keeping the consistent ones. The tool should also produce output in PSL, SAM, or BAM.

Thanks!