breseq can be a good option for you as bacterial genome is haploid. Check this paper https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-1039. However BBMap's callvariants.sh natively supports haploid genomes; the default ploidy is 1. It has been used for mutation study in E coli.

Thanks a lot ! 

Use Mutect2 from GATK package for best results

java -jar GenomeAnalysisTK.jar \

-T MuTect2 \

-R reference.fasta \

-I:tumor tumor.bam \

-I:normal normal.bam \

[--dbsnp dbSNP.vcf] \

[--cosmic COSMIC.vcf] \

[-L targets.interval_list] \

-o output.vcf

I used before GATK as Snijesh suggested but the analysis afterwards was a little unconvenient because the SNP calling was designed for eukaryotes. I do believe they've updated but i'm not sure. Or maybe now there is another tool for the variant filtering that can be used in this pipeline. Maybe R :p. 

The advantage is that i found it quite user friendly because it had quite a lot of options superwell explained in the webpage. 

Also, I heard about an R package called DEseq but i didn't use it myself. 

Good luck :D

GATK is optimized for diploid genome .If you want to use GATK you should use GATK with the updated version of haplotype caller which can now be set to ploidy =1. See the link for better understanding and how to use https://approachedinthelimit.wordpress.com/2015/10/09/variant-calling-with-gatk/. perhaps you can check this biostar page where similar problem has been discussed https://www.biostars.org/p/47860/

.

I find Sequencher from http://www.genecodes.com/ really user friendly. You can insert your own reference sequence and then compare the sequences by nucleic acid and manipulate the sequence (for ex. add insertions or deletions) to visualize the best possible alignment.

I really like Torsten Seemann's approach, "snippy"

Easy, fast and ready to go outputs

https://github.com/tseemann/snippy

The tool mentioned by Eric JC Gálvez looks impressive. But always take error rate into consideration.

Thanks all of you for your answers. I have many things to try now it is really cool ! :-)