Importing genome into IGV.

Preparing reference file.

Convert GenBank file to GFF/GFF3

login1$ module load bioperl

GFF

bp_genbank2gff --file input.gbk --stdout > output.gff

GFF3

login1$ bp_genbank2gff3.pl input.gbk

Convert Genbank file to Fasta

bp_seqconvert --from genbank --to fasta < input.gbk > output.fasta

Index Fasta file.

samtools index input.fasta

IGV

Click on File -> Import Genome and you should be presented with the following window.

Enter the ID and Name of the Genome you are working with and select the path to your *.fasta file (the index, *.fai file needs to be in the same directory), then select the path to your *.gff file for the Gene File.