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We're really interested in places in the genome where we think there are mutations. In the Variant calling tutorial we identified such locations but lacked a good way to visualize them. This is your opportunity to visualize them. We have already transferred the SRR030257.vcf file back to your local computer, but before we can visualize them, we need to (guess what?) index it.

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It will look like nothing has happened aside from the appearance of "Done" in the messages box, but you can now close the "Run" window and choose File > Load from File. If you navigate to your IGV directory, you will now see a brand new SRR030257.vcf.idx file. You can now load the SRR030257.vcf file, and it will show up as a new track near the top of your window.

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• Zoom in using the slider in the upper right. Do this until you see mapped reads and finally individual bases appear.
• Navigate by clicking and dragging in the window. This is how you move left and right along the genome.
• Navigate more quickly. Use page-up page-down, home, end.
• Jump to the next point of interest. Click on a track name on the left side of the window (Ex: bowtieSRR030257.vcf), to select it. 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 track.
• Jump right to a gene. (If you have gene features loaded.) Type its name into the search box. Try "topA".
• Load multiple BAM alignments or VCF files 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". Experiment with the other options.
• Change the appearance of reads. Right click on a BAM track and choose "show all bases" and "expanded". Experiment with the other options.

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