then by all means use 100% silicon caulking. Be careful not to get it on the wood area too much because its not paintable. But they do have some paintable new silicon caulk out now, but I have not tried it, I do know its expensive.
silicon is more flexible than glazing.
I agree with Dan on his comment, but if your glass meets the stops and you did not apply caulk when constructing, then you may need it to slide and shed the water off and away from the cracks between the glass and the stops.