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.  This tool is free to download and runs on Mac or Windows.

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 GABBR1 gene.

Steps:

1. Download and install the Integrative Genome Viewer from the Broad Institute.
2. Select "Human hg18" or "Human hg19" as the reference genome
3. Get some data: File -> Load from Server… -> 1000 genomes -> Alignments -> CEU Trio WGS -> select those 3 samples
4. Navigate to the rightmost exons of the GABBR1 gene
5. 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
6. Load and look at the SNP track: File -> Load from server -> Annotations -> Variants and Repeats -> 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?)