BWA MEM - which reads were mapped by mate-pair rescue?

[Flo1000]

Is there a way to tell which reads were mapped by mate rescue?
I learned that in BWA results there should be a XT:A:M tag in that case, but in my sam files I can't find any XT tags at all...

[Flo1000]

For those who are interested: Apparently, there is no way to tell if a read was mapped by mate pair rescue. From the BWA mailing list:

For bwa-backtrack, rescue is performed after mapping, but for bwa-mem, rescue is tightly integrated with mapping. The hits resulted from rescue and from single-end mapping are mostly indistinguishable.

[Brian Bushnell]

What do you plan to use that information for, anyway?

[Flo1000]

The authors of this paper suggest that "Simply removing SNVs for which 7% or more of the mapped reads were mate-rescued increased the validation rate [..] without eliminating any TPs". I wanted to give it a try within our pipeline.

[Brian Bushnell]

Assuming that paper was based on bwa-aln rather than bwa-mem, its results should have little bearing on bwa-mem, since they do rescue differently. But you can avoid rescue altogether simply by mapping all the reads as single-ended rather than paired to see if you get better results.