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From the main window of IGV, click on File -> → Import Genome... and you should be presented with the following window.
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From the main window of IGV, click on File -> → Load from File.... Choose bowtie.sorted.bam
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You can do this from within IGV:
- Choose File -> → Run igvtools....
- Choose "index" from the commands drop-down menu.
- Select your *.vcf file (Ex:
bowtie.vcf) for "Input File" - 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 see a brand new bowtie.vcf.idx file. You can now load the file bowtie.vcf, and it will show up as a new track near the top of your window.
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Workflow 2: Viewing Human Genome Data in IGV
If you've made it through the other exercises on your own data, take a look at some human genome re-sequencing data where the files can be loaded directly from public databases.
Advanced exercise: human data scavenger hunt
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- Download and install the Integrative Genome Viewer from the Broad Institute.
- Select "Human hg18" as the reference genome
- Get some data: File -> → “Load from Server…” -> → 1000 genomes -> → CEU and YRI trios
- Navigate to the GABBR1 gene and the rightmost exons
- Zoom in until you find the SNP
- Load and look at the SNP track: File -> → Load from server -> → Annotations -> → Variants -> → dbSNP
This is whole genome coverage data; later we'll look at exome data.
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