To begin your submission, click "Submit Challenge Entry" at the top of this page. The submission screen will ask for a title, a description, and a VCF file for your entry.
Start by providing a short title for your submission entry, then fill in the description. In your description, please identify whether you are participating as an individual or as part of the team (and, if it is a team effort, don’t forget to identify the members of your team). Explain the pipeline used to obtain the results, and identify the name, version and command-line parameters of the mapper and variant caller invoked in your pipeline. Discuss what INFO or FORMAT fields can be used to calculate the allele frequency. The description entry field supports the Markdown syntax. Don't worry if you don't get it perfect right away -- you can always go back and edit this description later.
If you opted to construct your pipeline on precisionFDA, and your VCF was generated by running one or more precisionFDA apps, the system will automatically prompt you to share the details of these executions when submitting your entry (see below). In that case, your description only needs to provide a high-level summary, because the exact software invocations will be available to the community via the system’s sharing mechanism.
In the submission input data section, click "Select file..." and choose the VCF file you'd like to submit. (In the popup click "Files", then tick "Only mine", then select your file).
Once you have entered a title and a description, and chosen a VCF file, the "Submit" button on the upper right corner will become active. Click the button to invoke the publishing wizard, which will prompt you to publish the VCF file so that others can see it (this is a requirement for participating in the challenge). If your VCF file was generated by running apps on precisionFDA (instead of being uploaded externally), the system will ask if you also want to publish the related job, app, and app assets.
After completing the publishing wizard, your VCF file will become public, and your entry will be officially submitted. The system will conduct an initial verification of your entry, by running software for validating VCF files, and other VCF comparisons. During that time, your entry will appear as "pending verification" under the "my entries" tab, but will not yet show up under the public "challenge submissions" tab. This step takes several minutes, and you can monitor it by clicking "View Log".
If your entry fails this step, it will be marked as "failed". You can click "View Log" to see some diagnostic information related to the execution of the verification software. Failed entries will not show up under the "challenge submissions" tab and will not be counted towards the challenge. (However, your VCF will have been made public -- but you are welcome to delete it).
If verification completes successfully, your entry will appear under "challenge submissions".
Successful entries cannot be revoked, but you can always submit new ones. You can also go back and edit the title and description of any entry.