Do you rely on ClinVar XML files for your application or analytical pipeline? We are significantly updating ClinVar’s XML format to support the inclusion of new somatic variation data provided by submitters. In the coming months, you may need to make changes to your tool or pipeline code to continue to use the ClinVar XML.
What will change?
- Update to the XML schema
- Updates to the VCF and tab-delimited files
- Look and feel of the website: new sections to display including somatic classifications
- New submission templates for somatic variants, and updates to the submission templates for germline variants
To prepare for these changes, please preview the submission spreadsheet templates, updated XSDs, sample XMLs, and supporting documentation on GitHub. Once the new XML format is available, we will continue to support the old XML format through the end of 2023. However, we encourage you to start the transition to the new XML format as soon as you can.
Sample files for the VCF and tab-delimited files will be posted on GitHub as they are available.
We are planning to add submission of somatic variants through the application programming interface (API) and the single-submission wizard in the next year. Stay tuned for more details!
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If you have questions or would like to provide feedback, please reach out to us at firstname.lastname@example.org.