text: user9521: I'm trying to run bwa on HiC data. This is the command I'm giving:
  bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq
  
  and here's the error message:
  mem: illegal option -- 5
  
  Supposedly, the 5SP option is for HiC data (cite), but my BWA isn't recognizing it. Anybody have any ideas? My initial thought is to update BWA to the newest version, but I don't want to mess with our replicatibility since I am new to the lab and don't want to be updating software when I don't need to. The server is a Mac Pro and bwa version is 0.7.12-r1039. Thanks.
  
  user2388: Your link with those command line options is 1 year old.  Looks like that version of bwa is 6 years old.  You probably should update.
  
  user-1: This option has been added in 0.7.16a, see https://github.com/lh3/bwa/releases, so consider updating.
  
original_text: 9521: <p>I'm trying to run bwa on HiC data. This is the command I'm giving:</p>
  <pre><code>bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq
  </code></pre>
  <p>and here's the error message:</p>
  <pre><code>mem: illegal option -- 5
  </code></pre>
  <p>Supposedly, the 5SP option is for HiC data (<a href="https://phasegenomics.github.io/2019/09/19/hic-alignment-and-qc.html" rel="nofollow noreferrer">cite</a>), but my BWA isn't recognizing it. Anybody have any ideas? My initial thought is to update BWA to the newest version, but I don't want to mess with our replicatibility since I am new to the lab and don't want to be updating software when I don't need to. The server is a Mac Pro and bwa version is 0.7.12-r1039. Thanks.</p>
   2388: <p>Your link with those command line options is 1 year old.  Looks like that version of bwa is 6 years old.  You probably should update.</p>
   -1: <p>This option has been added in 0.7.16a, see <a href="https://github.com/lh3/bwa/releases" rel="nofollow noreferrer">https://github.com/lh3/bwa/releases</a>, so consider updating.</p>
  