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Exploring Reads in IGV

Contributors: Gavin Band, Annie Forster

Getting the data​

In this tutorial you are going to be inspecting read alignments in a program called Integrative Genomics Viewer, or IGV for short. IGV is a very handy piece of software which allows you to visually inspect alignments across the genome.

First you will need to download IGV. You can find the software here - please download and install it now.

For this tutorial we will use sequencing data from P.falciparum malaria parasites. If you completed the earlier tutorial on paired-end sequencing, or the pipelining tutorial you will already have some aligned BAM files which you can use for this. For this tutorial you should load (at least) these files:

  • QG0033-C.bam
  • QG0041-C.bam

You are also welcome to load and look at others as well.

Note

Alternatively, my versions of the aligned files can be found in this folder.

An easy way to load these into IGV is to use the File -> Load from URL option. Then paste in the link to the BAM file.

Alternatively you can download the .bam and .bai files to your computer first.

If you followed the snakemake tutorial, you should also be able to look at:

  • Your coverage (.bedgraph) files for the above samples. (Although this isn't very important because IGV shows you coverage anyway.) You can find them in this folder if you don't have them already.

  • Your variants.vcf.gz file containing the variant calls from Octopus. (If yours doesn't work, this may be due to an Octopus issue that has now been fixed. I filtered out the problem variants in my version which you can try instead.)

Loading data​

To load these files into IGV, choose File -> Load from File... from the menu. You should be prompted to download the appropriate reference; “Pfalciparum3D7” should already be available from the provided selection. (If you're not prompted, make sure you are using the Pfalciparum3D7 (v9.0) genome. This should appear in the drop-down box at the top left of the window. If not, click on the dropdown and choose ... and then select P. falciparum 3D7 (V9.0) from the list).

Load in the BAM files for QG0033-C.bam and QG0041-C.bam now, as well as the variants.vcf.gz file if you have it. Once the data is loaded you're ready to go and view the reads.