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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
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SAM flag explanation #418

Closed weishwu closed 3 years ago

weishwu commented 3 years ago

Where can I find the explanation of each flag in the SAM output of Bismark, such as ZC, ZR, XL, XA, XB and YD?

FelixKrueger commented 3 years ago

I'm not sure whether Bismark reports all of the optional flags you mentioned above...

XA and XB can be optionally the number of non-bisulfite mismatches, but the others are not output by Bismark to my knowledge.