Preheat oven to 375°. Line baking sheets with parchment or a silicone baking mat.
Whisk together the flour, crushed pretzels, baking soda and salt in a small bowl and set aside.
Combine the brown sugar, peanut butter, shortening, milk and vanilla in a mixing bowl. Beat at medium speed until well blended. Add the egg and beat just until blended. Reduce speed to low and add the flour mixture gradually, mixing just until combined. Using a rubber spatula, stir in the chocolate chips.
Use a medium cookie scoop (or 2 tablespoons) to scoop dough and roll into a ball between the palms of your hands. Place on the baking sheets, about 2 inches apart. Dip the tines of a fork into a cup of water and make a crisscross patern on the cookies, flattening them slightly. Repeat dipping the fork in water as necessary if it starts to stick to the dough (I did it every few cookies).
Bake for 8 minutes or until set and beginning to brown around the edges. Cool for 2 minutes on the baking sheet before removing to a cooling rack. Store in an airtight container at room temperature for up to a week.