BWA mem has the -S
and -P
tags for skip mate rescue and skip pairing; mate rescue performed unless -S also in use.
What do these do? I presume -P
aligns read pairs independently of each other. Is that correct?
And what does -S
do?
Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. It only takes a minute to sign up.
Sign up to join this communityBWA mem has the -S
and -P
tags for skip mate rescue and skip pairing; mate rescue performed unless -S also in use.
What do these do? I presume -P
aligns read pairs independently of each other. Is that correct?
And what does -S
do?
Using -SP
is equivalent to running bwa mem
on each of the two mates as if they are single-end reads, but it formats the output as a proper paired-end output, i.e. with all pair-related flags added properly. Without -SP
, by default bwa mem
forces an alignment of a poorly aligned read if its mate is aligned somewhere. -SP
turns off the forced alignment. We use -SP
for mapping Hi-C reads.
If one read maps and the other doesn't, BWA attempts to rescue the other read by performing Smith-Waterman alignment with the unmapped mate, -S
disables this mate rescue.
-P
does indeed disables pairing, but mate rescues is still enabled - I think -P
disables the setting of the proper pair flag. If you set -P
and -S
, BWA maps the paired reads essentially as single reads.