converting annovar format file to maf by annovarToMaf

Question

[Zahra]

Hi,

I have annovar format file and want to convert it to maf , and to this aim, I use the annovarToMaf:

library(maftools)
var.annovar <- system.file("extdata", "ann_test.txt", package = "maftools")
var.annovar.maf <- annovarToMaf(annovar = "ann_test.txt", 
                                Center = 'CSI-NUS', refBuild = 'hg19', 
                                table = 'refGene', MAFobj = TRUE )

But no .maf file is created by this code. How can I get the output as a maf file?

Thanks for any help.

[KH]

Should you be calling annovar = var.annovar rather than annovar = "ann_test.txt" in your annovarToMaf function?

[Zahra]

Dear Kyle,

Thanks for your reply. when I use annovar = var.annovar rather than annovar = "ann_test.txt" I receive the error below :

Error in FUN(X[[i]], ...) : 
  Input is empty or only contains BOM or terminal control characters

and I don't know how to fix it.