They probably won't cover it unless you paid for an optional Road Hazard insurance...... Generally warranties only cover defects in the tire itself and a bolt through the tire wouldn't qualify.
Sorry........
That being said, is it through the tread or the sidewall? If it's through the tread, it should be repairable. I had a screw in one of my Michelin tires and took it to a Goodyear store and they fixed it right up.
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