Why does vcf2maf filter out CNV / Fusion/ ProcControl / RNAExonVariant ?

[lakhujanivijay]

I have a vcf file which have few rows with following type of data and I could observe that all of this is being filtered out.

grep -v "^#" sample1_pateint1.vcf | grep -Po "SVTYPE=\w+"  | sort | uniq -c
      1 SVTYPE=CNV
     94 SVTYPE=Fusion
      2 SVTYPE=ProcControl
      4 SVTYPE=RNAExonVariant

My command is :

vcf2maf.pl --input-vcf sample1_pateint1.vcf --output-maf sample1_pateint1.maf --ref-fasta genome.fa --filter-vcf 0 --vep-path /home/bioinfo/variant-effect-predictor-87-0/bin/ --custom-enst isoform_overrides_uniprot.txt --tumor-id sample1

Can you tell us why is this happening?