Is it possible to use samtools to identify complex mutations caused by e.g. UV mutagenesis?
samtools is good at identifying single, isolated mutations (e.g. single transitions and transversions in sequencing reads), but is it capable of identifying neighboring (i.e. consecutive) mutations?
The case I am interested in is UV mutagenesis, which can cause consecutive transitions, going from CT in a wild-type genome to TC at the same positions in in a mutant genome. I have ~50X Illumina coverage of a mutant genome, and can "see" this complex mutation (using samtools tview and zooming to the locus), but can't find arguments that allow me to identify each consecutive mutation via samtools mpileup and bcftools; I'd like to capture these positions in VCF files. I've fiddled with gap opening and extension parameters, but I don't think this is technically a "gapped" problem.
Any insight here?