How to plot datasets from VarScan2 in R.

[pablosantamarta]

Hi everybody,

I'm using VarScan2's Somatic Mutation Calling function and the output are two files with a large number of columns. I wanna represent graphically two columns (normal_var_freq(column 7) and tumor_var_freq(column 11)) form one of both with R and it was impossible for me. It is driving me mad!

If someone could help me, or tell me something about this, I'd be very gratefull!

Thanks in advance.

[Jane M]

One idea is to keep only the mutations in which you are interested by using a bash script, for example somatic or LOH.
But if you are interested in germline mutations, you won't maybe be able to read everything in R because that are the more frequent mutations...