Stockeo allows you to update variant barcodes. Barcodes can also be used as an alternative variant identifier when product SKUs are not available in the feed or when SKUs from the feed do not match those in Shopify.
To use barcodes as the variant ID, add the Barcode field to the Data Mapping section. Then click the gear icon next to the field and enable Use as variant ID.
Setting a barcode as an alternative variant ID in Stockeo
Once this is done, remove the SKU field from the Data Mapping section.
Removing the SKU field from the Data Mapping section in Stockeo
You can also use metafields to identify variants in Shopify.