In BWA-MEM what's the best way to discriminate reads mapping uniquely from those mapping in multiple positions? The XT tags that we used in BWA are no longer available. We are thinking about classifying as uniques the reads having XS:i:0 (suboptimal alignment score of 0). Someone is also suggesting to use a difference threshold between AS and XS. This would require a somewhat heavier parsing of the file, but we can do that if the improvement of results is significant. Which of the two methods is better? Are there other, better approaches?