Summary and Schedule

This lesson is a hands-on introduction to visualizing genomic data with the Integrative Genomics Viewer (IGV), a free desktop application for exploring genomic datasets. It is designed for people who are new to genome browsers but who already have some familiarity with common genomics file formats and concepts (chromosomes, genes, reads, variants).

Across a series of hands-on exercises, learners load a reference genome, load their own genome from a FASTA file, explore aligned sequencing reads (BAM) and candidate SNPs, precompute coverage data with igvtools, explore RNA-seq splice junctions with Sashimi plots, and explore population variant data from a VCF file.

Prerequisite

Prerequisites

1. Learners should be comfortable with basic genomics terminology: chromosome, gene, exon/intron, sequencing read, and variant.

2. Learners must install IGV (desktop) before the workshop starts. See the setup instructions for download links and instructions.

3. Learners must download and unzip the workshop data before class starts. See the setup instructions for the download link.

This lesson’s exercises, slides, and sample datasets are adapted from the IGV team’s BroadE workshop materials (Broad Institute, April 2017) by Jim Robinson and Helga Thorvaldsdóttir. If you use IGV itself in published work, see igv.org for the current recommended citations.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Introduction to IGV	What is IGV and when would I use it? What kinds of genomic data can I explore with a genome browser? What file formats does IGV work with?
Duration: 00h 20m	2. IGV Basics	How do I load a reference genome and some example data into IGV? How do I move around the genome at different zoom levels? How do I read the sequence and gene tracks?
Duration: 01h 10m	3. Loading Your Own Genome	How do I view my own genome, rather than one of IGV’s built-in hosted genomes? What do I lose by loading a genome from a FASTA file instead of one of IGV’s packaged genomes?
Duration: 01h 30m	4. Viewing Alignments and SNPs	How do I inspect individual sequencing reads that support a candidate variant? How can I tell a real SNP apart from a technical artifact? What does a BAM alignment record actually contain?
Duration: 02h 15m	5. Precomputing Coverage with igvtools	Why does my coverage track go blank when I zoom out? How do I precompute coverage data so it is visible at any zoom level?
Duration: 02h 40m	6. Viewing RNA-seq Data	How do I see which exons are spliced together in RNA-seq data? How do I compare splicing patterns between two samples or tissues? Why do RNA-seq reads look different from the DNA reads in the previous episode when aligned in IGV?
Duration: 03h 20m	7. Viewing Variants and Genotypes	How does IGV display variants and genotypes from a VCF file? How can I compare variant patterns across groups of samples, such as populations?
Duration: 03h 55m	8. Viewing Structural Variants	How can paired-end reads reveal deletions, fusions, and inversions? How do I confirm a candidate structural variant in IGV?
Duration: 04h 30m	9. Viewing Long-Read Sequencing Data	How does IGV handle long reads differently from short Illumina reads? How do I tell real signal from raw sequencing error in noisy long reads? How can long reads and read phasing help interpret structural variants and repeat expansions? Can IGV view a file that lives on a remote server, without downloading it first?
Duration: 05h 00m	10. Wrap Up	What have I learned, and where can I go next with IGV?
Duration: 05h 10m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Software: IGV desktop

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This lesson uses the IGV desktop application (not igv.js or IGV-Web).

1. Go to https://igv.org/doc/desktop/#DownloadPage/ and download the version for your operating system. IGV requires Java, and the downloads for Windows and macOS bundle a compatible Java runtime, so no separate Java install is needed.
2. Install and launch IGV to confirm it opens before the workshop starts.
3. You will need an internet connection the first time you launch IGV and whenever you load data hosted on the IGV server (used in the IGV Basics episode). The rest of the lesson uses data files stored on your own computer and does not need an internet connection.

Data

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The exercises use a small set of example genomics files (a chromosome sequence and index, a gene annotation file, sample BAM alignment files, and a population VCF file). Download igvData.zip (~95 MB) and unzip it into a convenient location, such as your Desktop or home directory.

After unzipping, you should have a folder called igvData with the following structure:

OUTPUT

igvData/
├── genome/
│   ├── chr1.fasta
│   ├── chr1.fasta.fai
│   └── refSeq_chr1.bed
├── snps/
│   ├── NA12878.SLX.sample.bam
│   ├── NA12878.SLX.sample.bam.bai
│   └── snp_calls.bed
├── vcf/
│   ├── ALL.apol1.sample.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf
│   ├── apol1_snp131.bed
│   ├── chr22.fa
│   ├── chr22.fa.fai
│   ├── hg19_chr22.genome
│   ├── integrated_call_samples_v3.20130502.ALL.panel
│   └── vcf_session.xml
└── svs/
    ├── hg38_chr21.genome
    ├── hg38.chr21.fa
    ├── hg38.chr21.fa.fai
    ├── NA19240.bam
    ├── NA19240.bam.bai
    └── svs_session.xml

The svs/ folder is used in the Viewing Structural Variants episode.

Keep track of where you unzipped the igvData folder — every exercise refers back to files inside it.