Phenotype Association Tools in Galaxy

SIFT

The intermediate steps are hidden from view as they complete, to make the history less cluttered. If you wish to see all of the steps in your history, click on the gear icon at the top of the history panel. A menu will open up, and one of the choices is Show Hidden Datasets.

To run SIFT, click on the SIFT tool and fill in the parameters as shown in the red box. In pgSnp format the alleles are always on the forward strand, so select "all on sense/forward/+ strand". By choosing "yes" for "Include comment column" we can keep column 4, which has the original alleles, in the output. We have also selected some of the optional fields to be included in our output (red arrows). Then click Execute. This tool may take some time to complete, so please be patient.

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