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?
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$\begingroup$ What version of BWA mem are you using? Have you looked at the manual that gets installed with bwa? "Please `man ./bwa.1' for the manual." $\endgroup$– BioathleteNov 26, 2018 at 19:59
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2$\begingroup$ 0.7.17; I did look at the manual page but the explanation is somewhat cryptic: "-P: In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair." $\endgroup$– juniper-Nov 26, 2018 at 20:11
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2 Answers
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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.
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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.
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$\begingroup$ What does "attempts to rescue" mean? Why would the second read map using Smith-Waterman and not using the original algorithm? $\endgroup$– juniper-Nov 27, 2018 at 1:33