IGV

Overview

The Integrative Genomics Viewer (IGV) is a high-performance desktop application for interactive visualisation of genomic data, developed by the Broad Institute. It displays aligned reads (BAM/CRAM), variant calls (VCF), signal tracks (bigWig, bedGraph), peak calls (BED, narrowPeak), and many other genomic file formats against a reference genome. IGV is widely used for visual inspection of alignments, variant validation, and generation of publication- quality screenshots. It also supports a batch scripting interface for automated visualisation of multiple genomic regions.

Installation

Download from the Broad Institute IGV page, or install via Bioconda:

mamba install -c bioconda igv

Basic Usage

Prepare files for IGV

BAM and VCF files must be sorted and indexed before loading into IGV.

samtools sort aligned.bam -o aligned.sorted.bam
samtools index aligned.sorted.bam
bcftools sort variants.vcf.gz -Oz -o variants.sorted.vcf.gz
bcftools index variants.sorted.vcf.gz

Launch IGV

igv.sh

Load files through the GUI (File > Load from File) or by passing them as command-line arguments.

Batch scripting

IGV supports batch scripts for automated screenshots and navigation. Save the following as igv_batch.txt and run it with igv.sh -b igv_batch.txt:

new
genome hg38
load aligned.sorted.bam
load variants.sorted.vcf.gz
goto chr17:43044295-43125483
snapshot brca1_region.png
goto chr13:32315474-32400266
snapshot brca2_region.png
goto chr7:117559590-117711986
snapshot cftr_region.png

Key Parameters

Flag / option	Description
`-b`	Run a batch script file for automated visualisation.
`-g`	Reference genome to load on startup (e.g., `hg38`, `mm10`).
`--igvDirectory`	Override the default IGV preferences directory.

Batch script commands:

Command	Description
`new`	Reset the session, clearing all loaded tracks.
`genome`	Load a reference genome (e.g., `hg38`).
`load`	Load a data file (BAM, VCF, BED, bigWig, etc.).
`goto`	Navigate to a genomic region (`chr:start-end`) or gene name.
`snapshot`	Save the current view as a PNG image.
`snapshotDirectory`	Set the output directory for snapshot images.
`sort`	Sort alignments (`base`, `strand`, `quality`, `insertSize`).
`collapse` / `expand` / `squish`	Change track display mode.
`maxPanelHeight`	Set the maximum pixel height for alignment panels.
`exit`	Close IGV after batch processing.

Expected Output

Interactive session:

IGV displays aligned reads as coloured horizontal bars against the reference genome. Variants are highlighted with colour-coded mismatches, insertions, and deletions. Coverage tracks show read depth across each region.

Batch script output:

brca1_region.png – screenshot of the BRCA1 locus on chromosome 17.
brca2_region.png – screenshot of the BRCA2 locus on chromosome 13.
cftr_region.png – screenshot of the CFTR locus on chromosome 7.

Screenshots capture all loaded tracks at the specified genomic coordinates and are saved in the current working directory (or the directory set by snapshotDirectory).