5 months ago by
United States, St. Louis, Washington University
Unfortunately GenVisR cannot accept VCF files at this time, for now the best approach will be to set the
fileType param to "custom", you will then be able to provide a data frame with the required columns "sample", "gene", "variant_class". You will also need to fill in the parameter "variant_class_order" which takes a character vector specifying the order preference for each variant class. For example if you had both a missense and nonsense mutation for the same gene/sample the one plotted would depend on the "variant_class_order" param.
There is a vignette specific to the waterfall function here as well that you might find usefull.