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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?

juniper-
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  • 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." – Bioathlete Nov 26 '18 at 19:59
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    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." – juniper- Nov 26 '18 at 20:11

2 Answers2

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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.

Soo Lee
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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.

h.mon
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  • What does "attempts to rescue" mean? Why would the second read map using Smith-Waterman and not using the original algorithm? – juniper- Nov 27 '18 at 01:33