I have a question concerning the generation of vcf (variant calling format) creation.
Does anyone know of a tool that would allow me to turn a multiple sequence alignment (containing reference and several variants) into a vcf file?
I have a multiple sequence alignment of a several cloned papillomaviruses. We know that the sequence of each individual genome are correct. I.e. all variations between the reference and these additional sequences represent naturally occurring SNPs (and not sequencing errors). I would like to extract the SNPs (and indels) from this alignment and create a vcf file. I hope this clarifies the problem! thanks again