In a small saucepan, combine the apples, vinegar, sugar, shallots, jalapeno, and garlic. Bring to a boil over medium-high heat. Reduce the heat to medium-low and simmer until the apples are translucent and soft and the vinegar has reduced by half, about 15 minutes. Remove from the heat and cool for at least 10 minutes. Once cool, transfer to a blender or food processor and puree until smooth, about 1 minute. Season to taste with salt and pepper.