SNP calling in a "case-control" setting
I wish to look for SNPs that are unique to my case samples, and do not appear in my control samples. To be more precise, their enrichment in the case samples should be significant. Something like a fisher's test.
I have many bam files of control samples, and many of cases. How can I run this?
This is bacterial DNA, so as far as we know, there is a single copy of each chromosome.