In the BWA man page, it is said that BWA should output a certain number of optional fields like X0, X1, XO, etc... However, when I run BWA mem, none of them are produced (some of them would be extremely useful for the project I'm dealing with right now).

Could someone shed lights on this?

Thanks
<p><a href="http://sourceforge.net/p/bio-bwa/mailman/message/31998697/">This thread</a> on the bio-bwa mailing list addresses your question. The summary is that `bwa mem` does not output those tags. Heng Li, the author, states:</p>

> Bwa-mem is unable to compute accurate X0 due to algorithmic restrictions. You can derive XM from CIGAR and NM. XT:A:M is not applicable to bwa-mem. XT:A:U and XT:A:R can be derived from mapping quality.