Hello,

We use Varscan to make our somatic mutation calls. I would like to know if I can use the vcf files generated by Varscan for SomaticSignatures or i would need to redo the variant annotation with the variantannotator? Can I extract the relevant info from Varscan output instead?
 

A minimal VCF file will sufficient for the analysis, as long as it has the details for defining groups of interest (see the vignette which groups according to cancer type). So there should be no need to preprocess the data with variant annotator or other programs.