<p>Using <code>-SP</code> is equivalent to running <code>bwa mem</code> 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 <code>-SP</code>, by default <code>bwa mem</code> forces an alignment of a poorly aligned read if its mate is aligned somewhere. <code>-SP</code> turns off the forced alignment. We use <code>-SP</code> for mapping Hi-C reads.</p>

CC BY-SA 4.0
2018-11-27T06:08:12.213Z
2018-11-27T06:08:12.213Z
Soo Lee
<p>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, <code>-S</code> disables this mate rescue.</p>

<p><code>-P</code> does indeed disables pairing, but mate rescues is still enabled - I think <code>-P</code> disables the setting of the proper pair flag. If you set <code>-P</code> and <code>-S</code>, BWA maps the paired reads essentially as single reads.</p>

CC BY-SA 4.0
2018-11-27T01:33:05.397Z
What does "attempts to rescue" mean? Why would the second read map using Smith-Waterman and not using the original algorithm?
juniper-
CC BY-SA 4.0
2018-11-26T20:24:57.097Z
2018-11-26T20:24:57.097Z
h.mon
<p>BWA mem has the <code>-S</code> and <code>-P</code> tags for <em>skip mate rescue</em> and <em>skip pairing; mate rescue performed unless -S also in use</em>. </p>

<p>What do these do? I presume <code>-P</code> aligns read pairs independently of each other. Is that correct? </p>

<p>And what does <code>-S</code> do?</p>

CC BY-SA 4.0
2018-11-26T19:59:25.410Z
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
CC BY-SA 4.0
2018-11-26T20:11:25.943Z
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-
<read-mapping><bwa>
What is mate rescue in bwa mem?
# What is mate rescue in bwa mem?

(Asked by: username_0 on 2018-11-26)

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?

**Tags:** read-mapping, bwa
> **Comments:**
> **username_1**: 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."  
> **username_0**: 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."_  

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## 2 answers

### Answer by username_2 on 2018-11-27. Score: 6 | Accepted answer

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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### Answer by username_3 on 2018-11-26. Score: 2

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.

> **Comments:**
> **username_0**: What does "attempts to rescue" mean? Why would the second read map using Smith-Waterman and not using the original algorithm?  

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