Technical Details

How a representative transcript is chosen.

A genomic location can be shared by multiple isoforms of a gene, therefore one variant can result in different consequences in different isoforms of a gene. For simplicity and convenience, it is customary to pick a "representative transcript (isoform)" of a gene and use it to denote the molecular consequence of a variant.

However, sometimes different researchers picked different isoforms as the representative one for a gene, which made communication and collaboration difficult.

In this context, MANE Transcripts were born. As a collaboration project between NCBI and EMBL-EBI, MANE transcripts aim to be a useful set of one representative isoform for one gene.

OakVar picks MANE Select isoforms as representative isoforms by default. Howver, with --primary-transcript option to ov run, you can pick a different isoform as a representative isoform of a gene as well.

--primary-transcript mane-clinical

will pick MANE Clinical Plus set transcripts as representative ones.

--primary-transcript file.txt

where file.txt is in the space-delimited format

GENE TRANSCRIPT

will pick the TRANSCRIPT as the representative one for the GENE. For the genes which are not defined in file.txt, MANE Select will be used if no other option is given to --primary-transcript, or MANE Clinical Plus will be used if mane-clinical is additionally given.

OakVar collects molecular consequence results for all the isoforms where a given variant maps in base__all_mappings column in the variant table in the result SQLite database.