co-mutation plot from vcf file
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?
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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