text: user9: 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?
  
  user1642: 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.
  
  user3745: 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.
  
original_text: 9: <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>
   1642: <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>
   3745: <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>
  