IGV: A quick overview
The Integrative Genome Browser (IGV) from the Broad Institute can be considered the microscope for the Bioinformatician.
IGV can be easily downloaded from the Broad Institute website.
It’s a Java application with a graphical user interface (GUI), and its concepts revolves around:
- Loading a reference sequence
- Adding tracks related to the reference sequence, such as:
- Alignments (BAM files)
- Genomic features, annotations (GFF, GTF, BED files)
- Variants (VCF files)
Load a reference sequence
The reference genome can be selected from a drop-down menu, which allows to select one of the many model organisms available, or we can load a FASTA file from our disk, using the “Genomes” :right_arrow: “Load genome from file…” menu.
Load some tracks
If we have sorted and indexed BAM files, VCF files or annotation files we can load them from the “File” :right_arrow: “Load from File…” menu.
We will see the results plotted.