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 BWAMEM BAM files. These reads are tagged with "SA:"
My problem is that I'm working with BAM files that are not BWAMEM 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 taggs. Are these XA: tagged reads equivalent to SA tagged reads?
In the context of CNV discovery. Split reads (with secondary alignments/ SA tags in BWAMEM) 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?