Hi,

I'm trying to use MSIseq R package but I'm facing some difficulties. I have MAF file (which was generated from a vcf file using vcf2maf tool) but I don't understand how should I use it.

I tried the following code:

test.mutationNum<-Compute.input.variables(my_maf_file_path,seq.len = num)

but I got the following error:

Please check if the following columns are in your data: Chrom, Start_Position, End_Position, Tumor_Sample_Barcode, Variant_Type.

The MAF file used has those columns, thus I thought that my MAF file needs some kind of parsing before usage, but I'm not sure.

Your assistance in this matter would be greatly appreciated.