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I have a vcf containing SNV and MNV (short indells or substitutions), I have annotated that file with annovar and in the resulting txt file I have this row:

chr7    140453136   140453137     AC   TT  exonic   BRAF    .     nonframeshift substitution              BRAF:NM_004333:exon15:c.1798_1799AA:p.V600K

If I convert the txt file in maf using annovarToMaf function of maftools bioconductor package I obtain NA as value for Variant_Classification field. In other words, the field is included in the original vcf file but it is converted into NA when saved as maf with maftools.

What is the correct value of the Variant_Classification field in a .maf file for non-frameshift substitutions like BRAF V600K?

I tried vcf2maf and that tool put Missense_Mutation as a value for Variant_Classification of BRAF V600K mutations.

I tried to download the .maf file of TCGA melanoma (that should contain BRAF V600K mutations) but the access to that file is restricted.

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  • $\begingroup$ Ok, try to make a reproducible example as it might be a bug on the maftools package. However I would first post this reproducible example here to see if there is a solution without involving changes on the package $\endgroup$
    – llrs
    Mar 7, 2019 at 12:08

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