Are XA: tagged reads == SA: tagged BWAMEM aligned reads?

Question

[QVINTVS_FABIVS_MAXIMVS]

I have a simple question. I am interested in reads with secondary alignments.

I have a script that will parse out reads with secondary alignments for bwa-mem BAM files. These reads are tagged with SA:

My problem is that I'm working with BAM files that are not bwa-mem aligned. If I search for SA tagged reads I return nothing.

However I noticed there are reads with a XA: tag with information nearly the same as SA tags. Are these XA: tagged reads equivalent to SA tagged reads?

In the context of CNV discovery. Split reads (with secondary alignments/ SA tags in bwa-mem) are informative. If the XA tag reads are "split reads" then I should be able to use them for CNV discovery.

Or am I missing the whole point of XA tags?

[Brian Bushnell]

XA is not a standard field, so the definition depends on the aligner. Which aligner are you using?

Answer 1

[Zev.Kronenberg]

XA are alternative alignments (~secondary hits).

SA are chimeric alignments (split reads)

You can also search for the 0x800 flag for the second alignment of the splitter.

Which version of BWA mem are you using?

The older version of BWA mem provides another flag XP, for splitters.

[xiaoleiusc]

What do you mean by "the second alignment of the splitter"? Does the number of reads with the 0x800 flag equals the number of reads with SA tag?