The way you do it is you discard a particular color channel (or pair of channels) from each eye.
So for standard red/cyan anaglyph you would discard the red channel from the left eye, and then discard the blue and green channels from the right eye. You can do this pretty easily with a full-screen pixel shader, for example.
However, keep in mind that image/video compression may result is some artifacts between the eyes, so you will likely not be able to obtain a ghost-free image. In addition, color reproduction would be poor compared to native stereo.
AMD Ryzen 7 1800X | MSI X370 Titanium | G.Skill 16GB DDR4 3200 | EVGA SuperNOVA 1000 | Corsair Hydro H110i
Gigabyte RX Vega 64 x2 | Samsung 960 Evo M.2 500GB | Seagate FireCuda SSHD 2TB | Phanteks ENTHOO EVOLV