2.2 KVar Submission

KVar Submission Workflow

The KVar submission process consists of five major steps, as outlined below.

⚠️ Note: Required fields are marked with an asterisk (*). Make sure all mandatory fields are filled in before submitting.

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1. Submission Info

In this step, submitters check whether BioProject and BioSample have already been registered.

• If pre-registered BioProject and BioSample accessions exist, they can be selected and linked to the submission.

• If no prior registrations are available, additional steps are provided to allow simultaneous submission of BioProject and BioSample within the same submission. For more information, refer to 2.1. BioProject & BioSample submission.

  • BioProject: Submitter & Project info step

  • BioSample: Package & Attribute step

In addition, submitters set the data release date by selecting either Release immediately or Release on a specified date (a calendar widget will be displayed for date selection).

Once all required information is completed, click Continue to proceed to the following step.

2. Study Info

This step collects study-level information related to the variant data, including the following:

• Specify the variant type to be registered (SNP or SV).

• Enter study title and description. If SV is selected, also choose the study type (Case-Control, Case Set, Control Set, Collection, Somatic, Tumor vs. Matched-Normal)

• Enter submitter information, including name, email address, affiliation, and department.

• Indicate the publication status of the study (Unpublished or Published). For published studies, provide the corresponding PubMed ID or DOI.

Once all required information is completed, click Continue to proceed to the following step.

3. File

In this step, submitters provide the path to the folder containing the variant files uploaded to GBox.

• Accepted file formats include VCF and Excel (.xlsx) files.

• For VCF submissions, compressed .vcf.gz files are recommended.

Please refer to Variation File Format Guide for the required upload file formats

4. KVar Metadata

This step involves entering structured metadata using an Excel-based template.

The following metadata sheet entities are required:

• SampleSet: Describes the grouping of subjects and samples included in the study.

• Sample: Contains detailed information about the subjects and samples.

• Experiment: Describes the experimental methods and analytical procedures used to identify variants.

• Dataset: Provides information about the generated variant dataset.

Metadata requirements differ slightly depending on whether the study is an SNP or SV submission.

Please refer to KVar metadata for detailed metadata fields for each sheet

Navigation Panel

1. [≡]: Enable/ disable the navigation panel

2. Data (Rows) navigation: Clink a row to navigate to that row (N: New, R: Saved, M: Modified, D: Deleted, E: Error)

3. Item (Columns) navigation: Clink a item to navigate to the at columns

4. [🔒]: Dock / undock the navigation panel

Ribbon Menu

1. [🔍Search]: Search within the spreadsheet

2. [🔖Download and Example standard submission form]: Download the standard submission form (.xlsx) and view examples

3. [🪟Toggle screen mode]: Enable / disable full screen mode

4. Spreadsheet Control area: → (Re-run) , ← (Undo) , + (Add row), - (Delete row)

5. [📤Upload metadata template file]: Upload a completed metadata template file

6. [📥Download this table]: Download the table including all entered data

Input Fields (Cells)

1. Memo: View a description of the selected item

2. Filter: Filter metadata entered for the selected item

3. Data Field: Enter data in the cell

   • [ ]: Direct input

   • [ ▼]: Dropdown selection

   • [ 🖋️]: Guided input by field type

   • [ ⬆️]: File upload

4. Sheet Tabs: Click a tab to move to the corresponding sheet

5. Review & Submit

In the final step, submitters review all entered information and uploaded files before submitting the completed KVar submission.

Once all steps have been completed, navigate to the Review & Submit step to verify the submission details and click Submit.

The system performs a final validation check, and if no issues are detected, the submission is successfully completed.

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After Submission

Submitted data are subject to administrative review.

• After review, the submission will be either approved and registered in KVar or returned (rejected) for revision.

• If revisions are required, submitters will be notified and can update the submission accordingly.