BWA XT:A:U and XA for same read?

SFAB · 11-19-2013, 09:33 AM

Apologies if this has been asked before, but I can't see an answer and can't seem to figure this out.

Looking at the BWA documentation I see that XT:A:U denotes unique, while the XA tag gives alternative mappings. That makes me think I shouldn't get both XT:A:U (which I'm understanding to mean a read that maps uniquely) and XA, a read with more than one mapping for the same read. However, looking at a BAM file generated by BWA using samtools, that is what I'm seeing, both the XT tag with U and entries in XA for the same read.

If anyone could explain this, it would be appreciated.

swbarnes2 · 11-19-2013, 09:42 AM

Is this read paired end?

I think what might have happened is that the read by itself might be ambiguous, but maybe with the information from the mate pair, it can be properly placed, and maybe one tag wasn't changed to reflect that?

Or is it possible that it maps to the one location, but is only a single base off of the others?

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11-19-2013, 09:33 AM	#1
SFAB Junior Member Location: UK Join Date: Aug 2012 Posts: 3	BWA XT:A:U and XA for same read? Apologies if this has been asked before, but I can't see an answer and can't seem to figure this out. Looking at the BWA documentation I see that XT:A:U denotes unique, while the XA tag gives alternative mappings. That makes me think I shouldn't get both XT:A:U (which I'm understanding to mean a read that maps uniquely) and XA, a read with more than one mapping for the same read. However, looking at a BAM file generated by BWA using samtools, that is what I'm seeing, both the XT tag with U and entries in XA for the same read. If anyone could explain this, it would be appreciated.

11-19-2013, 09:42 AM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	Is this read paired end? I think what might have happened is that the read by itself might be ambiguous, but maybe with the information from the mate pair, it can be properly placed, and maybe one tag wasn't changed to reflect that? Or is it possible that it maps to the one location, but is only a single base off of the others?