Dear all, please could you advise : how does MAFTOOLS treat the annovar files with the gene names ? For examples, shall I have a file (below), the questions would be :

> head(var.annovar.maf)
          Hugo_Symbol Entrez_Gene_Id   Center NCBI_Build Chromosome
1:             WASH7P             NA STANFORD       hg38       chr1
2:     FAM138D,OR4F16             NA STANFORD       hg38       chr1
3:             ZYG11B             NA STANFORD       hg38       chr1
4: LINC01206,FLJ46066             NA STANFORD       hg38       chr3
5: TRHDE,LOC101928137             NA STANFORD       hg38      chr12
6:              TMTC2             NA STANFORD       hg38      chr12
   Start_Position End_Position Strand Variant_Classification Variant_Type
1:          21282        21282      +                    RNA          SNP
2:         282266       282266      +                    IGR          SNP
3:       52783942     52783942      +                 Intron          INS

-- 1. how does MAFTOOLS parses  the Hugo_Symbols "FAM138D,OR4F16  " or "LINC01206,FLJ46066", and

-- 2. what does IGR means in the Variant_Classification column ?

thank you !

1. It doesn't parse Hugo_Symbols and uses them as is. I think in your case its due to annovar annotations, it assigned them to two different genes (or synonyms of same gene, not sure). I would highly suggest to use VEP as its much smarter and picks a prioritized canonical transcript. Or even better is use maf2maf (https://github.com/mskcc/vcf2maf). It wraps around VEP and does the rest for you (But I find its installation a bit frustrating).  

2. IGR -> Variant is in Intergenic Region