All right, those are easy to work with. First, the software you need:
AviSynth
Anaglyph plugin for AviSynth
FFMS2 plugin for AviSynth
x264 (32bit 8bit-depth; if you'd rather use 64-bit, it's slightly more complicated)
Yamb
Install AviSynth and put the plugin DLL files in the plugin directory (something like C:\Program Files\AviSynth 2.5\plugins), and install Yamb.
Create a folder and put your video file and x264.exe in it.
Open Notepad and paste this into it:
FFVideoSource("filename.mp4")
ConvertToRGB32(matrix="Rec709")
Anaglypher(Crop(0,0,-(Width()/2),0), Crop(Width()/2,0,0,0), \
0.456, 0.500, 0.176, \
-0.040, -0.038, -0.016, \
-0.015, -0.021, -0.005, \
-0.043, -0.088, -0.002, \
0.378, 0.734, -0.018, \
-0.072, -0.013, 1.226)
ConvertToYV12(matrix="Rec709")
This script may produce a very tall, thin video for some side-by-side 3D videos. Show me a screenshot of the video so I can be sure it's correct. Replace filename.mp4 with the real filename, and save it as script.avs in the folder with the video files and x264.exe.
Open Notepad again and paste this into it:
@echo off
REM Speed preset. From fastest to slowest, they are:
REM
REM ultrafast, superfast, veryfast, faster, fast, medium, slow, slower,
REM veryslow, placebo
REM
REM Use the slowest that you're willing to wait for.
set speed=veryslow
REM Quality level. It ranges from 1 to 51. Lower numbers give better quality,
REM but also larger files. Higher numbers are worse quality, but smaller files.
REM
REM Most people prefer between 15 and 20.
set quality=15
x264 --profile high --preset %speed% --crf %quality% --vbv-maxrate 24000 --vbv-bufsize 24000 --level 4.1 -o anaglyph.h264 script.avs
pause
Adjust the speed and quality settings as you see fit, and save it as run.cmd.
Double-click on run.cmd and wait for it to encode your video. If it's a full-length movie, it can take a very long time! You can stop it partway through if you're just checking to see how well it works.
Once it's done, open Yamb and choose to create a new MP4 file. Open the h264 file and the original MP4 file. Uncheck the video track from the MP4 file, type in a file name, and click next. Once it completes, you can close Yamb.
I think I covered everything. Let me know if anything doesn't work.
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