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I have a vcf containing SNV and MNV (short indells or substitutions), I annotate that file whit 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.

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

I tied 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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  • $\begingroup$ Perhaps because this is not my field I find the question a bit terse. Could you please expand it a bit more? For instance what is the BRAF V600K substitution? I found this link but this is about mutations. Have you looked up at the file format specifications? Isn't there any example with these field filled? $\endgroup$
    – llrs
    Mar 7 '19 at 10:35
  • $\begingroup$ thanks @llrs, I edited the question ting to be more clear. The link you found describe the mutation, what I need is to understand what is the correct value of the filed Variant_Classification in a maf file for such kind of variants. $\endgroup$
    – mox
    Mar 7 '19 at 11:06
  • $\begingroup$ Is your problem that the field is included in the original vcf file but it is converted into NA when saved as maf with maftools? $\endgroup$
    – llrs
    Mar 7 '19 at 11:12
  • $\begingroup$ @llrs exactly. Now I tried vcf2maf and that tool put Missense_Mutation as a value for Variant_Classification of BRAF V600K mutations $\endgroup$
    – mox
    Mar 7 '19 at 11:55
  • $\begingroup$ 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 '19 at 12:08

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