co-mutation plot from vcf file

Question

[prabha]

Hi,

I am doing variant analysis on around 200 samples, I have merged the vcf files produced for each sample into one vcf file and eventually I had identified the variants.

I am trying to produce a co-mutation plot for around 600 variants identified using this maftools (https://github.com/PoisonAlien/mafTools). Initially I convert the tab file containing only the 5 required fields to a maf file. But I encounter an error when I try to use this maf file to produce co-mutation plot using oncoplot function. The error is

Error in `[.data.frame`(tot.muts, , c("Hugo_Symbol", "Tumor_Sample_Barcode",  :
  undefined columns selected

Kindly provide your suggestions to solve this problem.

Also is there a way to obtain just the sample id, gene name, variant from the vcf file?

[a.james]

Hello Prabha,

Also is there a way to obtain just the sample id, gene name, variant from the vcf file?

You need to annotate your vcf file for this.Use can try annovar for this

I am trying to produce a co-mutation plot for around 600 variants You cab try this blog..

Hope this helps