I am trying to use the --custom option of vep with version 100.4
vep --input_file myfile.vcf.gz ...... --fasta myfasta.fasta --custom custom.gff.gz,,gff
My custom.gff.gz file has two lines, a gene and a transcript, and the file format:
1 Ensembl gene 1000 5000 . + . ID=ENSG01234;Name=GENE1
1 Ensembl transcript 1100 4900 . + . ID=ENST01234;Parent=ENSG01234;Name=GENE1-001;biotype=protein_coding
Result returns a variant that I expect to see, like:
## custom.gff.gz : custom.gff.gz (overlap)
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position
Protein_position Amino_acids Codons Existing_variation
Extra CNV_1_1300_4000 1:1301-3000 duplication - - - intergenic_variant - - - - - - IMPACT=MODIFIER;VARIANT_CLASS=duplication
Although everything about my files seems correct, and the command returns the variant that is specified inside my GFF file, in the output I can not see any information about the gene name or transcript that I included in my GFF.
What do you think could be the reason for this? I am curious about your thoughts. Thanks!