Content Comparison

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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:

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 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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Data from the CEU trio from the 1000 Genomes Project can be found directly from the Broad's server for IGV. Find the dbSNP accession number for the SNP apparent in There are now MANY genomes available this way - one of the original family trios are represented in samples NA12892, NA12891, and NA12878 (mom, dad, child respectively).

Find one or more dbSNP accession numbers for SNPs apparent in one of the two 1000 genomes project trios in the intron between exons 8 and 9 of the GABBR1 geneGABBR1 gene.

Steps:

1. Download and install the Integrative Genome Viewer from the Broad Institute.
2. Select "Human hg18" as the reference genome
3. Get some data: File → ? “Load from Server…” → ? 1000 genomes → CEU and YRI trios? CEU -> select those 3 samples
4. Navigate to the GABBR1 gene and the rightmost exons
5. Zoom in until you find the SNPsome SNPs
6. 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.

Is there an alternate allele in the child which correlates with one or both of the parents? (i.e. - do genetics work?)

From here...

You can also use IGV to visualize RNA-seq data in later tutorials.

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