I am trying to analyze Illumina sequenced bacterial data from known species to find mutations and I am stuck. Which tool I should use? It seems like half of the tools hugely over-represents the number of variants, even with strict parameters (Breseq, Freebayes) and the other half finds barely any variants (Snippy, VarScan) even with very loose parameters. I read several papers about this and tried a lot of software but still I feel like all the tools belong to either category. What can I do?