I am working with RNA viruses for which I need great depth in each position in order to correctly call variants. At the moment I have my pileup formats derived from mpileup algorithm, however when I try to convert them to vcf files using VarScan the Minimum read depth can be set only up to 200, and I need at least 100.000. Is there a way to do it through the galaxy server or I need to do it only with commands? If so, I would appreciate the command with any explanations necessary to do it as I am not command savvy.
Linked topic Mpileup with vcf output? How to change galaxy to older version?