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Question: Maftools required fields do not match with vignette
0
gravatar for Silvia
13 months ago by
Silvia0
Silvia0 wrote:

Hi,

I just tried to load my MAF file with maftools, but although the vignette states that the required fields are only 7 (Hugo_Symbol, Chromosome, Start_Position, End_Position, Variant_Classification, Variant_Type and Tumor_Sample_Barcode), I got the following error messages:

Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants,  :
  missing required fields from MAF: Reference_Allele

Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants,  :
  missing required fields from MAF: Tumor_Seq_Allele2

Could you please make these two fields (Reference_Allele and Tumor_Seq_Allele2) not required, to be coherent with the package vignette?

Thank you!

Silvia

ADD COMMENTlink modified 13 months ago by anand_mt60 • written 13 months ago by Silvia0
0
gravatar for anand_mt
13 months ago by
anand_mt60
anand_mt60 wrote:

Hi Silvia,

Reference_Allele and Tumor_Seq_Allele2 are essential fields for some of the analysis such as signature and APOBEC enrichment estimation. Apologies on my part, I will update the vignette. But for now, you can just add two columns to your MAF file (you can populate them with NA or leave them blank) with title `Reference_Allele` and `Tumor_Seq_Allele2` and it should work fine (except for signature analysis). Hope this helps.

-Anand.

 

ADD COMMENTlink written 13 months ago by anand_mt60
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