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
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