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.