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.
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.
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