Females have two X chromosomes and are designated XX. Males have one X and one Y chromosome and are designated XY.
From your question, there is certainly a chance you can impregnate your wife naturally if the only issue is a deletion of a portion of the Y chromosome. Depending on your exact type of Y chromosome deletion and the extent of deletion, you may have either no decreased chance of impregnating your wife or you may have have a 50% reduction in impregnating your wife. In the former, you would have normal daughters but your sons would also likely carry your Y chromosome deletion. In the latter, we are assuming that your Y chromosome deletion has no impact on your X chromosome but the Y chromosome is incompatible with life. Therefore you can only have daughters as only your sperm with X chromosomes are viable. The remaining 50% of your sperm containing the mutated Y chromosome is incompatible with life.