GFF, BED and VCF are commonly used annotation file formats. GFF and BED files normally contain gene and other sequence features, while VCF files are used for variant call data. As these files generally do not contain sequence, you must provide the sequence to import the annotations on to.
To do this, you can either import the sequence from a fasta file at the same time you import the annotation file, or you can import the file onto an existing sequence in your Geneious database.
When you import the annotation file you will be prompted for the sequence in one of two ways:
1. If there is a fasta file with the same name, and in the same folder as the annotation file, Geneious will ask if you wish to import this file as well.
2. If Geneious does not find a matching fasta file in the folder, it will ask where you want to get the sequence from:
If you already have the sequence(s) in Geneious and have selected the sequence documents prior to importing the annotation file, choose Use one of the selected sequences.
If you have not selected the sequence(s), but are in the folder containing the sequence(s), choose Find a sequence with the same name in this Geneious folder.
If you have the sequence in fasta format and Geneious has not already offered to import that file, choose Import the sequence from a file.
If Geneious cannot find a matching sequence it will import the annotations onto a blank sequence with ? for all bases.
Note that it is critical that the sequence names match the sequence IDs in the annotation file, otherwise Geneious will not be able to determine which sequence to import the annotations onto.
You must also ensure that you import the file onto the same sequence that was used to generate the annotations. For example, if you have a GFF file for the human genome build GRCh37, then you must use this version and not GRCh38. If you use the wrong reference sequence the annotations may be in the wrong location.
Once the file is imported, the annotations will be displayed as a track on your sequence file. If you cannot see the track, check it is enabled under the Annotations and Tracks tab to the right of the viewer.