I would love to create a waterfall plot of my tumor-normal pairs with GenVisR but my files are in vcf format. I tried maftools to convert, but I couldn't get it to work.
Now I'm considering using Washington University's GenomicModelingSystem to get the MGI annotation format for convenience. But looks like I'm gonna need to downgrade my ubuntu to 10.04 to use it. Is there no other way for me, other than to use WashU's GMS? What annotation tool is recommended for GenVisR?
I'm willing to start over from fastq files. Could somebody show me the ropes?