Losing info when reading maf file

[eibol1]

Hi there,

I am reading a maf file, converted with vcf2maf.pl from https://github.com/mskcc/vcf2maf

I converted it from a VCF which only have PASS variants like this:

perl vcf2maf.pl --input-vcf /Users/abelgd/Desktop/training_bioinfo/VCFs_pipeline_curro/tejidos_vcfs_PASS/descomp/PCT75.filtered.PASS.vcf --output-maf ~/Desktop/PCT75_pass.vep.maf --tumor-id PCT75T.tumor --normal-id PCT75P.normal --ref-fasta /Users/abelgd/.vep/homo_sapiens/107_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa --vep-path ~/ensembl-vep --ncbi-build GRCh38

The original VCF have 27 variants, but when I see the maf object it only has 4 variants.

Does anyone know why is this happening? Maybe is something about VEP or vcf2maf command? My VEP version installed is v_107 from the official website: https://www.ensembl.org/info/docs/tools/vep/script/index.html