I have 14 interest proteins and want to know how does their genetic status change during cancer (which somatic mutations occur in their genes?). To this aim, I started analysis on the VCF files of 80 patients. I proceeded according to the following steps:
- Annotation of VCF files
- Using a bed file to separate my interest genes among all variants
- Filtering the mutations that occur in exonic loci
And now I do not know how to continue my analysis? Can I visualize them with an Oncoplot?
Thank you for letting me know if you have any suggestions for further analysis or point me to related articles.