2015年4月15日星期三

XT tag in BWA SAM output 

In BWA SAM option field, there is a user reserved tag:

XTType: Unique/Repeat/N/Mate-sw

which annotated as follow:


XT:A:U unique read.
XT:A:R multiple mappings for that read.
XT:A:M (one-mate recovered) , one of the pairs is uniquely mapped and the other isn't.
XT:A:U flag alone and discarded any others tag values.

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