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.