Both graphics APIs (OpenGL and DirectX) devise a well defined pipeline in which several stages are programmable. These programmable stages require to take a fixed minimum amount of data and are supposed to do a well defined range of operations on it, and output some defined minimum output, so that data can be passed on to the next stage correctly. It seems as if these pipelines are designed to work with only a limited amount of types of geometric data, which in the case of both D3D and OGL are vertex data and texture co-ordinates. 

But, if given a case when the application I plan to make doesn't use vertices ( or even voxels ) to represent its geometric data and does not exactly do transformations or projections or rasterisation or interpolation or anything like that, such limitations of the APIs or the pipeline make things difficult. 

So, is there a way in which we can change graphics pipeline in a way so that the functionality of what each stage does to the data and the type of data that is outputted in each stage is changed to my advantage? If not, then is there a way by which I can use the 'raw' API functions to construct my own pipeline? If not, then please mention why it isn't possible.