Maf File Bar Code

Question

[Manuel Sokolov Ravasqueira]

Hi,

I am running the GATK Best practices Pipeline over targeted sequence with reference hg19. After running the entire pipeline. I used maftools to view the file and realized that the file has no Tumor_Sample_Barcode.

However I have clinical data related to that patient and have information about the patient Id (Tumor Sample Bar Code).

 Tumor_Sample_Barcode Frame_Shift_Del In_Frame_Del Missense_Mutation Nonsense_Mutation 
 Splice_Site  RNA Intron 3'UTR  IGR
 1:          __UNKNOWN__              20            1               379                14          10 2294  10489   283 6027
 5'Flank Silent 5'UTR DE_NOVO_START_IN_FRAME COULD_NOT_DETERMINE 
 DE_NOVO_START_OUT_FRAME total
 1:    1759    198   287                      2                   1                       1 21765

How can I add tumor sample bar code to Maf File ?

Best Regards. Manuel

Answer 1

[Zhenyu Zhang]

MAF is just a TSV file. You can use bash, R, or even excel.