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Old 06-03-2014, 09:10 AM   #58
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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W,

I use the "XT:A:R" tag to indicate that a read is ambiguously mapped and XT:A:U to indicate unambiguously mapped. If you say "ambig=all" then the threshold for printing secondary alignments is more liberal than the threshold for deciding an alignment is ambiguous. So, even "unambiguously" aligned reads will sometimes have secondary sites printed - the best one, and others that are "decent" even though they are sufficiently worse than the best site that I classify the best site as unambiguous.

So if you add up all of the primary alignments with XT:A:U, you should get the same numbers as the program reports. Sorry that it's a custom tag (that is also used by bwa), but there's nothing in the official flag bits or official tags to indicate whether an alignment is ambiguous, and the SAM spec doesn't say anything about the presence of secondary alignments indicating ambiguity. It's really a subjective judgement.
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