So, i use WBA mem to align my reads (from NGS panels) to reference genome. My reads align to two different, but very similar regions. I want to prevent align these reads to non target region when i use BWA mem. I hope that will make MQ of my reads > 0 because they will be aligned only to target region. Maybe i can use bed-file contained regions that BWA should ignore to align reads or something like that... I did not found something like that in BWA docs.