I'm new to this kind of projects, so I would like some guidance on how to start.
I've tried the full GATK pipeline for human samples and now I have to work in a bacterial project. I have the reference genome and 10 recently sequenced strains by Illumina 2x100bp technology. While running GATK on human samples, I used lots of SNPs databases in different steps. However, I do not have SNPs databases for this bacteria. So how should I proceed? What approach (pipeline) should I go on with? Should I first create a SNP database using the strains I have and then use it in the whole process?
I'm installing GKNO to give it a try.
Thank you very much in advance.