Question regarding GTF or GFF usage. about ensembl-vep HOT 3 OPEN

Hi @eprdz ,

Thank you for reaching out. The logic for fetching biotype makes sense to be consistent across GFF and GTF file. We are going to work on this and keep you updated.

Kind regards,
Likhitha

from ensembl-vep.

Thank you for answering me.
I was wondering if you know which of the 2 is the correct approach or if there is a third option.
Can you point me in the right direction (documentation, a colleague) to find out more about this so I can get a timely solution for this?
By now, what I do is execute AGAT to transform GFF files to GTF v.2.5 files in order to overcome the need of having the biotype in the 9th column.
Do you think this is feasible?
Thanks in advance for your help.

from ensembl-vep.

Hi @eprdz ,
Thank you for your patience.

In GFF files, biotype is fetched from "biotype", "transcript_type", "transcript_biotype" of the attribute fields, there are also some additional checks for biotype. In the future update, if the biotype is still empty in spite of all the checks, then it will be fetched from the source column (similar to GTF).
Converting to GTF file should be feasible in the meantime.

Kind regards,
Likhitha

from ensembl-vep.