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I did it in onCameraFrame():

    public Mat onCameraFrame(CameraBridgeViewBase.CvCameraViewFrame inputFrame) {
    mRgba = inputFrame.rgba();
    Imgproc.cvtColor(mRgba, mRgb, Imgproc.COLOR_RGBA2RGB); //the apply function will throw the above error if you don't feed it an RGB image
    sub.apply(mRgb, mFGMask, -1); //apply() exports a gray image by definition
    Imgproc.cvtColor(mFGMask, mRgba, Imgproc.COLOR_GRAY2RGBA);

    return mRgba;
}

The global vars needed:

 private BackgroundSubtractorMOG2 sub = new BackgroundSubtractorMOG2(10, 25, false);
private Mat mRgb=new Mat();
private Mat mFGMask=new Mat();
private Mat mRgba=new Mat();

Credits to Austin from Stack Overflow.