Adding TAGS from custom GTF about ensembl-vep HOT 2 OPEN

Hey @cdiaz45,

VEP currently only allows to keep fields from a custom VCF file, fields from other custom annotation formats are ignored. I added this to our backlog and will see what we can do about this.

In the meantime, could you show me a sample of your GTF? Thanks!

Best,
Nuno

from ensembl-vep.

Thank you so much for the quick reply: This is an extract from the gff which is the latest one from gencode:
##gff-version 3
#description: evidence-based annotation of the human genome (GRCh38), version 44 (Ensembl 110)
#provider: GENCODE
#contact: [email protected]
#format: gff3
#date: 2023-03-01
##sequence-region chr1 1 248956422
chr1 HAVANA gene 11869 14409 . + . ID=ENSG00000290825.1;gene_id=ENSG00000290825.1;gene_type=lncRNA;gene_name=DDX11L2;level=2;tag=overlaps_pseudogene
chr1 HAVANA transcript 11869 14409 . + . ID=ENST00000456328.2;Parent=ENSG00000290825.1;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1
chr1 HAVANA exon 11869 12227 . + . ID=exon:ENST00000456328.2:1;Parent=ENST00000456328.2;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;exon_number=1;exon_id=ENSE00002234944.1;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1
chr1 HAVANA exon 12613 12721 . + . ID=exon:ENST00000456328.2:2;Parent=ENST00000456328.2;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;exon_number=2;exon_id=ENSE00003582793.1;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1
chr1 HAVANA exon 13221 14409 . + . ID=exon:ENST00000456328.2:3;Parent=ENST00000456328.2;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;exon_number=3;exon_id=ENSE00002312635.1;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1
chr1 HAVANA gene 12010 13670 . + . ID=ENSG00000223972.6;gene_id=ENSG00000223972.6;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;level=2;hgnc_id=HGNC:37102;havana_gene=OTTHUMG00000000961.2
chr1 HAVANA transcript 12010 13670 . + . ID=ENST00000450305.2;Parent=ENSG00000223972.6;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2
chr1 HAVANA exon 12010 12057 . + . ID=exon:ENST00000450305.2:1;Parent=ENST00000450305.2;gene_id=ENSG00000223972.6;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=1;exon_id=ENSE00001948541.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:37102;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2

from ensembl-vep.