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Advanced exercise: 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).

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  and install the Integrative Genome Viewer from the Broad Institute. See  Download.
2. Select "Human hg18" or "Human hg19" as the reference genome from the top left drop down (you may need to select "more" to have hg19 as an option)
3. Get some data: File > Load from Server… > 1000 genomes > Alignments > CEU Trio WGS > select those 3 samplesACB > exome > HG01880
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 3Load and look at the SNP . (Hint look just to the left of the 2nd exon).
6. What type of library is this?
7. If you knew this was a cancer patient, consider how strongly you would think this may be a potentially causative mutation.
8. Imagine it was actually in the exon rather than just into the intron... would that make you consider it more?
9. 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.

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rs29220, rs29222, rs28359988, rs76688565, there might be more in the locus; I got tired of looking.

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1. 1.3.7
2. The track may load with the Refseq genes, making it useful to resize that window to view both the gene and the dbSNP information simultaneously.
3. Consider if this makes you think it more likely or less likely that this is a causative mutation.

From here...

samtools faidx NC_012967.1.fasta
samtools view -b -S -o bowtie/SRR030257.bam bowtie/SRR030257.sam
samtools sort bowtie/SRR030257.bam bowtie/SRR030257.sorted
samtools index bowtie/SRR030257.sorted.bam

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