ENSEMBL VEP custom annotation with GFF file

Question

[gdm01]

Hello,

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!

Answer 1

[Emily]

Can you add the exons or CDS, example:

1 Ensembl gene 1000 5000 . + . ID=ENSG01234;Name=GENE1
1 Ensembl transcript 1100 4900 . + . ID=ENST01234;Parent=ENSG01234;Name=GENE1-001;biotype=protein_coding
1 Ensembl exon        1200  1300  . + . ID=exon1;Name=GENE1-001_1;Parent=ENST01234
1 Ensembl exon        1500  3000  . + . ID=exon2;Name=GENE1-001_2;Parent=ENST01234

I think only the transcripts are not enough.