I am analyzing a dataset that has paired tumor-normal data. I called variants using Varscan2 somatic, which provides really nice information on whether the variant is germline, LOH, or somatic. I converted the Varscan2 ".snp" output file to VCF format, and tried running it through snpEff on default settings. This produced a result, but it seems that the information on variant type (germline, somatic, LOH) is not in the snpEff annotation file.
I have also been looking into the "- cancer" option for snpEff, but it looks like this would just be re-doing the work that Varscan has already done.
Has anyone else run into this as a similar issue? Would it make more sense to use a different annotation software? Something else I was considering was that Varscan2 gives the option to output separate files based on variant type (LOH, germline, somatic), but this seems convoluted, so I'm guessing there must be an easier way I'm not aware of.