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Workflow 2: Viewing Human Genome Data in IGV
If Now that 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 databasesfamiliarized yourself with IGV using a "simple" bacteria, let's look at something a "little" more complex: the human genome.
Advanced exercise: human data scavenger hunt
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See this page for the human data scavenger hunt
Data from the CEU trio from the 1000 Genomes Project can be found directly from the Broad's server for IGV. 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).
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- Download and install the Integrative Genome Viewer from the Broad Institute. Download
- Select "Human hg18" or "Human hg19" as the reference genome
- Get some data: File > Load from Server… > 1000 genomes > Alignments > CEU Trio WGS > select those 3 samples
- Navigate to the rightmost exons of the GABBR1 gene
- Zoom in until you find some SNPs - they might be in exons or introns; there is also at least one example of a short insertion variant between exons 2 and 3
- Load and look at the SNP track: File > Load from server > Annotations > Variants and Repeats > dbSNP
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