I am mostly working with primate data, but I doubt if the best practice for such data is still the best for bacteria given higher divergence between bacterial strains. Here are two possible ways to do SNP/INDEL discovery for bacteria:
Just like variant discovery for mammals, we map reads to the reference strain with a standard mapper and run GATK/samtools/in-house tools to find variants. If this is still the case, which mappers and SNP callers do you use? How do you change the default settings?
Do de novo assembly first and then align contigs to the reference strain to find variants. If this is the case, which assembler (velvet, soapdenovo or abyss?) and aligner (mummer?) do you use?
There much be other ways of analyzing data I do not know...