Content Comparison

...

We're really interested in places in the genome where we think there are mutations. You can load the VCF file to check out those spots, but first you need to (guess what?) index it.

You can do this from within IGV:

1. Choose File -> Run igvtools....
2. Choose "index" from the commands drop-down menu.
3. Select your *.vcf file (Ex: bowtie.vcf) for "Input File"
4. Click the "run" button.

It will look like nothing has happened, but you can now close the "Run" window and choose File -> Load File. If you navigate to your IGV directory you will now have a brand new bowtie.vcf.idx file. You can now select load the file bowtie.vcf, and it will show up as a new track at the top of your window.

Tip: You can index BAM and FASTA files the same way if you haven't already created indexed indexes for them.

Navigating in IGV

There are a lot of things you can do in IGV. Here are a few:

• Jump to the next point of interest. Click on a track name on the left side of the window (Ex: bowtie.vcf), then it will be selected. You can then use control-f and control-b to jump forward and backward within that list of features. Try this on the variant calls.
• You can jump Jump right to a gene by typing . Typing its name in to the search box. Try "topA".
• Navigate more quickly. The home and end keys jump a page backward and forward.
• You can load Load multiple VCF and BAM alignments at once. Try this to compare a few different regions between the bowtie and BWA results.
• Change the appearance of genes. Right click on the gene track and try "expanded".
• Change the appearance of reads. Right click on a BAM track and choose "show all bases" and "expanded".

Exercises

• Check out the rbsA gene region? What's going on here?
• What is going on in the pykF gene region? You might see red read pairs. What does that mean?