I have paired-end bam files (exomes) for two groups each with multiple individuals (all from one species, non-viral). I am interested to get information as mentioned here http://www.ark-genomics.org/bioinformatics/virome Would it be possible to do with `Rsamtools`? I am in the process of learning `Rsamtools` and getting stuck with how to process all files together to get final output. My aim is to retrieve genes and SNPs from this species as compared to reference (with same genus). Kindly guide.