LocusZoom DNAnexus App
The LocusZoom DNAnexus app visualizes GWAS result files stored on the DNAnexus platform.
The LocusZoom app visualizes GWAS result files stored on the DNAnexus platform including an interactive Manhattan plot, QQ plot, and a table of high p-value loci, as well as standard LocusZoom regional plots. It supports the use of GRCh37 and GRCh38 reference genomes.
This DNAnexus app is based on hosted LocusZoom codebase, and uses a virtual machine, so it incurs compute charges during use. The GWAS results stay on the DNAnexus platform while using this app.
LocusZoom app is launched from the Tools Library menu as shown below:
A user can specify an array of GWAS results files to visualize as app's input. These files will show up in the GWAS file dropdown once the app is running. Note that other GWAS results can be visualized by entering file IDs of a platform file with the GWAS results in the input entry field.
After selecting which GWAS results file you want to view, a set of interactive dialogs that recognize common GWAS results formats will appear on screen. You can select more specific settings for the GWAS visualization, and select Next when you are done.
Importing the GWAS results file may take some time. The Analyze tab will display the file in "Pending" state that will transition to a "Ready to View" state once your GWAS results are ready to visualize.
One your file is done loading, clicking on the name of the file in the Analyze tab will bring up the LocusZoom interactive analysis environment.
Clicking on a loci on the Manhattan Plot or in the Top Loci table will zoom into the loci:
Note that this app does not save its state, so you will need to follow the steps above to re-import the GWAS results file in another instance of LocusZoom app if you wish to view the visualization again.