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In bwa mem, when the insertion size cutoff is set as [a, b] (using the -I option), only the reads with the insertion size of [a + 1, b + 1] will have the change to be labeled with "proper pair" (flag 2).
In bwa mem, when the insertion size cutoff is set as
[a, b]
(using the-I
option), only the reads with the insertion size of[a + 1, b + 1]
will have the change to be labeled with "proper pair" (flag 2).Reason:
The
dist
variable (the distance between R1 and R2 starting position) instead of theinsertion size
was used to compare with the cutoff.https://github.com/lh3/bwa/blob/master/bwamem_pair.c#L239-L242
Solution:
From:
To:
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