I have many VCF files (each for different bacteria spp.) for SNPs/INDELs that I just want to extract SNPs/INDELs from. Then I will like to compare these variants in each file against each other to find which SNPs/INDELs are common/absent in each file. I'm new to this kind of analysis, and would be pleased if someone could advice me on any available tools or computational steps/scripts (R, Python, Perl) most appropriate for what I want to achieve.
Thanks in advance.