what does "XT:M" in BWA output mean?

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orionzhou

Member

Join Date: Sep 2009

Posts: 14
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#1

what does "XT:M" in BWA output mean?

11-13-2010, 08:03 PM

XT:U => Unique alignment
XT:R => Repeat
XT:N => Not mapped
XT:M => Mate-sw

so what the hell is this "Mate-sw" type alignment?

PS:
#define BWA_TYPE_NO_MATCH 0
#define BWA_TYPE_UNIQUE 1
#define BWA_TYPE_REPEAT 2
#define BWA_TYPE_MATESW 3

Last edited by orionzhou; 11-13-2010, 08:08 PM.
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nilshomer

Nils Homer

Join Date: Nov 2008

Posts: 1285
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#2

11-13-2010, 08:27 PM

Try

Code:

grep MATESW *.c

since you already started searching through the source code.

You'll see that it occurs when a read is fixed due to paired end rescue. Also, don't double post.
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