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Seems quite inefficient but it works for me (for now):

//get the camera parameters
Camera.Parameters parameters = camera.getParameters();
int width = parameters.getPreviewSize().width;
int height = parameters.getPreviewSize().height;

//convert the byte[] to Bitmap through YuvImage; 
//make sure the previewFormat is NV21 (I set it so somewhere before)
YuvImage yuv = new YuvImage(data, parameters.getPreviewFormat(), width, height, null);
ByteArrayOutputStream out = new ByteArrayOutputStream();
yuv.compressToJpeg(new Rect(0, 0, width, height), 70, out);
Bitmap bmp = BitmapFactory.decodeByteArray(out.toByteArray(), 0, out.size());

//convert Bitmap to Mat; note the bitmap config ARGB_8888 conversion that 
//allows you to use other image processing methods and still save at the end
Mat orig = new Mat();
bmp = bmp.copy(Bitmap.Config.ARGB_8888, true);
Utils.bitmapToMat(bmp, orig);

//here you do whatever you want with the Mat

//Mat to Bitmap to OutputStream to byte[] to File
Utils.matToBitmap(orig, bmp);
ByteArrayOutputStream stream = new ByteArrayOutputStream();
bmp.compress(Bitmap.CompressFormat.JPEG, 70, stream);
byte[] bytes = stream.toByteArray();
File pictureFile = getOutputMediaFile();
try {
    FileOutputStream fos = new FileOutputStream(pictureFile);
    fos.write(bytes);
    fos.close();
} catch (IOException e) {
    e.printStackTrace();
}