Importing genome into IGV.

Preparing reference file.

Convert GenBank file to GFF/GFF3

module load bioperl

GFF

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

GFF3

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

Import to IGV.

From the main window of 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.

Preparing alignment file.

If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.
To get import an alignment into IGV we first need to convert the file into BAM format, sort and then also index the file.

Convert to BAM format.

samtools sort -bS input.sam output.bam

Sort.

samtools sort input.bam sorted_output

Note: The second parameter passed here is a prefix and will be suffixed with .bam by samtools.

Index

samtools index input.bam

Import to IGV.

From the main window of IGV, click on File -> Load from File and select your input.bam file.

IGV

After importing your reference genome and loading an alignment file, your screen should look similar to the following:

And you are now free to investigate different areas and their alignments in the genome.