I have aligned around 3 varieties against 5 different reference genomes. Now I have several BAM files. What I want to do next is to see if there are different SNPs in different varieties and references (in the same region of course), or if there are some regions where there are no reads or exactly same reads. In other words may be having BAM file results as a table could be a good option. I dont think variant calling (.vcf) is useful in this case. Does anybody know how to transform a BAM file into a parsable table?
Any suggestions could be very helpful.