Figure 8.5:
Selecting a reference sequence when importing BED, GFF or VCF files
BED files, GFF files and VCF files contain annotation information which can be imported into Geneious Prime. These files often do not contain the sequence itself, so when you import the file you will be prompted for the reference sequence as shown in Figure 8.5 .
Note that if you choose “use a sequence in the selected folder”, or you have a sequence list or more than one sequence selected and choose “use a sequence in the selected documents”, then your sequence’s name in Geneious must match the sequence name in the first column of the BED, GFF or VCF file. If you select a single sequence and choose “use a sequence in the selected documents” then your annotations will be imported onto that sequence regardless of whether it matches the sequence name in the file.
For more information on these file formats, see:
Note that in BED format the first base is numbered 0 rather than 1, and Geneious accounts for this when it imports the file so your annotations will be shifted 1 bp to the right compared to their positions listed in the BED file.