Adding or updating multiple variants in Curate

To add or update (v100.40.0+) multiple variants in Curate, upload a CSV file with variant information.

Follow the instructions below.

Adding multiple variants to Curate

How to add or update a large set of variants in Curate

1

Prepare a CSV file with variant details. See CSV requirements for details about supported fields and formatting.

Batch updates (v100.40.0+)

Starting with v100.40.0, you can update existing variants in batch mode. To do this, include the Update column in the CSV file and set its value to true for each variant you want to update.

2

Open Curate Variants.

3

Select Add new ( symbol) in the navigation panel.

4

Select Switch to batch.

5

Confirm that the genome reference selected in the navigation panel (GRCh37 or GRCh38) matches the reference used in the CSV file.

6

Upload the CSV file.

Important: Do not leave the page until file upload is complete, as leaving will cancel the upload. The upload is finished when file validation results appear.

7

Review the file validation results:

• If validation succeeds: Proceed to the next step (confirming file upload).

• If validation fails:

  • Select Download the CSV file to download the CSV file with an added Error column detailing any issues.

  • Fix errors in either the original or annotated file. The Error column in the annotated CSV file is ignored during re-upload.

  • Select Cancel.

  • Return to the previous step (uploading the file).

  

  Select Download the CSV file to download your original file with an added Error column explaining the issue.

8

Select Upload to finalize the file upload.

9

After uploading the file to Curate, a notification appears with a Download report link. Download the upload summary file to review the status of each variant's upload.

Important: If you don't download the upload summary before closing the notification or leaving the page, it won’t be accessible later from the UI. You will need to contact Illumina Support for assistance.

Upload results:

• Success: Variant added with all details.

• Partial success: Variant added, but some fields were ignored.

• Duplication: Variant not added because it already exists in Curate.

• Update: Existing variant updated with new information.

• Fail: Variant not added due to overlap or intergenic location.

Handling existing variants during batch upload

• If Update is set to false (default), existing variant in Curate is marked as Duplication and is not updated.

• If Update is set to true, existing variant in Curate is updated with the new information from the CSV file.

Result: Variants are added, partially added, updated, or skipped. Review the upload summary to confirm the outcome for each variant.

Note: Updating existing variants with ACMG data does not change the ACMG schema version.

Alternative ways to add variants to Curate

• Manually add a single or several variants by specifying their details. Learn more

• Export a variant directly from a case in Analyze. Learn more