Summary and Setup

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.

Software: IGV desktop

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

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.