Index Variations Based on Category

I’d like to be able to run the indexer based on product category so I can set different values for different categories. At the moment I have 2 very large categories that are going to be product only and then some smaller categories that I want to be showing the variations. When I run the indexer I can only set options to apply to all and then I have to manually correct the smaller categories, rather than being able to run the update base don category level.