I have read many posts regarding this question. The XT, XA tag doesn't seem to be used anymore by BWA mem, so I can't use them to identify uniquely mapped reads.
Some posts said that multiple hits are to be assigned a quality score of 0. However, I don't have any links to confirm if this is still true. Does anyone know where I can confirm this?
Does anyone know how to tell if a read is uniquely map from the result of BWA-mem alignment? Thank you.