I want to create a animation on every other frame I have a photoshop filter applied. Reading the documentation I can’t stop photoshop from applying the filter to all the frames, is it even possible ?
If your ultimate output is GIF, then simply treat your animation as individual frames and create everything necessary for each one in layer groups. Then simply show and hide the groups as needed for the animation frames. I know it’s overkill, but it’s the easiest way to get each frame independent of the other.
If you will apply any filter on a layer it will effect all the frames. you will have to create new layers for each frame
I have solved it ! 
Great! Would you mind telling us how?
Ryangm has the answer