The FIle Repository Tool allows users to narrow their queries within the database by clinical- and file-based filters to specify which files they can use for their research.
If you load the File Repository tool from the Explore Data tool, the results of the query you began building will be loaded. We encourage users to begin by using the Explore Data tool first.
If you load the File Repository first, the full contents of the Kids First Data Resource Portal will be summarized at the top of the page.
The File Repository tool, loaded from the Explore Data tool, will bring in the results already generated from the first query.
File Filters, on the left side of the window, can be used to further narrow your query to specific files you are interested in. For example, if you are interested in sequence variants, you could choose to look at VCF or gVCF files in a cohort. If you have other research questions, you could start with the aligned reads in BAM or CRAM format to begin your analysis.
In the Filter tab on the left side, scroll down to Data Type or File Format to further refine your search.
After a filter is applied, the File Repository will automatically update to reflect these file formats.
Use the Browse All button at the top to search through all available data filters. Descriptions of all possible filters can be found on the File Repository Filter List.
Note: As you refine your query, the URL in your browser window will also update. This URL can be copied and shared with collaborators to quickly point them toward these same files that you identified.
Information about the results of your query are listed in center of the File Repository window. Definitions for the default columns are displayed below.
More columns can be added to the view by selecting the Columns drop-down button.
File Browser Column Definitions
When you are satisfied with your filters and ready to start analysis, there are a number of paths you can take depending on the final size of your query.
Individual files can be downloaded to a local disk or sent to Cavatica for analysis using the Actions buttons adjacent to each file name.
With a large number of files, send them to Cavatica for analysis or bulk download using the Analyze in Cavatica button.