Preheat oven to 350°. In a large bowl with an electric mixer on medium speed, beat butter with sugars until smooth. Beat in egg, peanut butter, and vanilla until well blended.
In another bowl, whisk together flours, wheat germ, oats, baking soda, and salt; stir or beat into butter mixture until smooth, scraping down sides of bowl as needed. Stir in chocolate chips.
Spread dough evenly in a buttered 8-inch square baking pan. Bake until pale golden brown, 25 to 30 minutes. Let cool on a rack about 10 minutes, then cut into 12 pieces. Let cool completely.
Note: Nutritional analysis is per serving.