Preheat oven to 350ºF. Line a baking sheet with a parchment paper or a silicone baking mat. Set aside.
In a medium size bowl, whisk together the flour, baking soda, baking powder, and salt. Set aside.
In a separate medium size bowl with a hand held mixer or the bowl of a stand mixer fitted with a paddle attachment, cream together the butter and brown sugar on medium speed. Scrape down the sides and bottom of the bowl with a spatula. Add the egg and vanilla extract, and beat again on medium speed until everything is combined and there are no lumps.
With the mixer on low, slowly add the dry ingredients to the wet ingredients in 2 additions, mixing thoroughly after each addition. Fold in chopped pretzels with a spatula.
Using a cookie scoop or a Tablespoon measuring spoon, drop rounded balls onto baking sheet. Bake for 10-12 minutes until sides just begin to brown (mine took exactly 11 minutes). Remove from oven and allow to cool on the baking sheet for 1-2 minutes before transferring to a wire rack to cool completely. Cookies stay fresh in an airtight container at room temperature up to 1 week. Baked cookies may be frozen up to 2 months. Balled cookie dough can be frozen, up to 2 months. Bake frozen on baking sheet for 11-13 minutes.