How to get vaf information column using annovartomaf

Question

[MS]

Hi,

I am trying inferHeterogeneity function in R.

I converted my annovar output to maf file using annovartomaf according to the toolsheet. But I can not get t_vaf containing vaf information.

I also don't have i_TumorVAF_WU.

My annovar output file has columns as given: "Chr Start End Ref Alt Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene Tumor_Sample_Barcode Func.refGene". I deleted some columns according to annovartomaf tutorial.

maf file includes:

 tumor.het <- inferHeterogeneity(maf = laml)
 [1] "Chromosome"             "Start_Position"         "End_Position"           "Reference_Allele"      
 [5] "Tumor_Seq_Allele2"      "Tumor_Sample_Barcode"   "Hugo_Symbol"            "Variant_Classification"
 [9] "tx"                     "exon"                   "txChange"               "aaChange"              
[13] "Variant_Type"           "sample_id"              "Gene.refGene"           "GeneDetail.refGene"    
[17] "ExonicFunc.refGene"     "AAChange.refGene"       "Func.refGene"          

Error in inferHeterogeneity(maf = laml) : 
  t_vaf field is missing. Use vafCol to manually specify vaf column name.

Could you please help me with how can I add this information to my object? Thanks.