Phenotype Association Tools in Galaxy

Joining on genomic intervals

We will do a join between the two datasets to get the predictions associated with our SNPs. We don't have a shared identifier to join on, so instead we will join together rows of the two datasets whenever their positions on the genome overlap. The result has all of the information from both datasets, for any position on the genome where there is data in both datasets.

In the Operate on Genomic Intervals section of the tool panel, click on Join. Then in the center panel, select the filtered SNPs from Part 1 as the first dataset and the PolyPhen-2 predictions as the second. We are only interested in SNPs that appear in both sets, so leave the default setting of doing an Inner Join. Then click Execute.

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