This challenge has been posted to the precisionFDA “Discussions” section. Discussion answers can include rich text formatting, as well as attachments such as files or comparisons. You can leverage this functionality to submit your entry by filling in your answer to the question.
In your answer’s text, 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). Write a description of 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.
If you opted to construct your pipeline on precisionFDA, and your VCFs were generated by running one or more precisionFDA apps, the system will automatically prompt you to share the details of these executions when publishing your answer (see below). In that case, your text 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.
Once you save your answer, it is initially private (and only visible to you). You can go back at any point and edit it, so we encourage you to start drafting it right away, and revise it as you make progress. Once you instantiate your answer, you can attach your VCFs and your HG001 comparison to it by visiting each item and clicking Attach, and selecting your answer. Your entry must contain two VCF files (one for HG001 and one for HG002) and the HG001 comparison (as outlined in the previous section) in order to be considered valid.
Once you are comfortable with your answer, you can publish it so that others can see it (and don’t worry – you can still edit it or update its attachments even after publication). When publishing, the system will ask if you want to publish the comparisons, as well as the VCF files that were input to the comparisons; please choose that option to ensure that these artifacts are shared with the precisionFDA community. Entries that do not have their comparisons and VCF files published will not be considered valid. If you used apps on precisionFDA (instead of generating these VCF files externally), please choose the option to share the underlying jobs, apps, and app assets.