Contradiction between MAPQ=0, XA tag and FLAG=256 for multiple alignment hits in BWA results
I intended to find all the non-primary alignments in the bam generated by bwa. After searching for solutions, I got different answers including using MAPQ=0, XA tag and FLAG=256. As far as I understand, these three indications are the same to tag not uniquely aligned read. However, the filtering using each criteria give contradictory result. For example, selecting by 'XA:' tag gives alignments of various MAPQ and FLAG value and vice versa. Is there anything I am missing for this case?
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I think the XA tag is used to report alternative alignment, not secondary alignment, the best way to get primary alignment should be using flag 256
Thanks, the link helps