BWA mem has the
-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
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-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
-S, BWA maps the paired reads essentially as single reads.