Entering edit mode
3.0 years ago
MS
▴
30
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.