Integrative Genomics Viewer (IGV) tutorial

Overview

The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.

Learning Objectives

In this tutorial, we're going to learn how to do the following in IGV:

• Create a custom genome database (usually used for microbial genomes) or load a pre-existing genome assembly (usually used for the genomes of model organisms and higher Eukaryotes).
• Load output from mapping reads to a reference genome.
• Load output from calling genetic variants.
• Navigate the view of the genome and interpret the display of this data.

Theory

Because NGS datasets are very large, it is often impossible or inefficient to read them entirely into a computer's memory when searching for a specific piece of data. In order to more quickly retrieve the data we are interested in analyzing or viewing, most programs have a way of treating these data files as databases. Database indexes enable one to rapidly pull specific subsets of the data from them.

The Integrative Genomics Viewer is a program for reading several types of indexed database information, including mapped reads and variant calls, and displaying them on a reference genome. It is invaluable as a tool for viewing and interpreting the "raw data" of many NGS data analysis pipelines.

Table of Contents

Workflow 1: Viewing E. coli data in IGV

Data files

You can start this tutorial two ways:

1. If you have an intro_to_mapping directory with output from the Mapping tutorial or the Variant calling tutorial, then you should use those files for part 1 of this tutorial. You can proceed with either one alone or with both.

2. If you do not have any results, you can use some "canned" ones that we provide. Copy the entire contents of this directory back to your local machine:

   /corral-repl/utexas/BioITeam/ngs_course/intro_to_mapping/IGV
   

    Help

   scp -r username@lonestar.tacc.utexas.edu:/corral-repl/utexas/BioITeam/ngs_course/intro_to_mapping/IGV .
   

   Then skip down to #Launching IGV.

Prepare a GFF feature file for the reference sequence

IGV likes its reference genome files in GFF (Gene Feature Format). Unfortunately, our old friend bp_seqconvert.pl doesn't do GFF. So, we're going to show you another tool for sequence format conversion called Readseq.

Readseq is written in java. To use it you need to first download the file readseq.jar linked from here.

To get this onto TACC easily, use:

wget http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq.jar

The general command to run the software is one of these:

java -jar readseq.jar
java -cp readseq.jar run

This should return the help for Readseq.

(Why the funny invocation? You are actually using the command java and telling it where to find a "jar" file of java code to run. The -jar and -cp options run it in different ways. It's pretty confusing.)

To do the conversion that we want, use this command: