Hello biostars -er, I have been reading several papers that they used Variant Effect Predictor (VEP) to assess the functional impact of somatic mutations and DrGAP tool to find out driver genes. And now, I am stuck with some questions, can anyone has experience with these give me answers.
For VEP, the paper said: "after we use VEP, the mutations were then divided into nine groups based on their functional impact, including frame shift indels, in-frame indels, missense mutation, nonsense mutation, nonstop muta- tion, RNA, silent, splice site and translation start site (TSS)"
I run VEP with my somatic mutation file, there are a lot of useful results appearing but I just see the variant sequence but no variant classification at all like that of the paper. How do I do to get the variant groups ?
For DrGap, it requires the user find the driver genes using R programming with its package. I do some reseaches but cant find the tutorials to use the DrGap in R. Can anyone give me the protocol to use it or code examples in R you used to run DrGAP package?
Thanks in advance.