Alignment tool that lists SNPs?

[mmarti12]

Hello,
I'm going to do GWAS among a subset of bacterial genomes that have a specific phenotype and I was wondering whether there's a tool that gives you the list of snps among them. I wouldn't like to use a reference to find the variations because in this case I'll miss the comparison of the genes that are not present in the putative reference. So I excluded comparative software like breseq.
Any suggestions?
Thanks a lot

[JohnN]

ParSNP from the Harvest suite?

https://harvest.readthedocs.org/en/latest/