Preheat the oven to 320˚F.
In a medium bowl, sift together the flours and baking soda.
In a separate bowl, cream together the butter and the sugars until light and fluffy. Beat in the eggs and vanilla. Slowly mix in the flour mixture until fully incorporated. Fold in the chocolate chips and pretzels.
Scoop the batter onto a prepared baking sheet. Place 1 whole pretzel on top of each cookie and bake for around 15-17 minutes, or until the edges are browned.