Sequence Variation Detection For Prokaryotic Genomes

I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).

Which sequence variation detection software that uses paired-end information is recommended for such a task? I only tried LifeScope's LargeInDel-Analysis tool, but apparently it's not suited for bacterial genomes (I would have thought that this is the easiest case...).