Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-12T05:17:58.757Z
Answers.LastActivityDate: 2020-10-12T05:17:58.757Z
Answers.UserDisplayName: swbarnes2
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-12T09:29:34.497Z
Comments.Text: You can use `conda` to install and test the desired version of `bwa` to test. This will not interfere with whatever version installed on the server.
Comments.UserDisplayName: haci
Tags: <bwa><hi-c>
Title: BWA doesn't recognize HiC options
ThreadText: # BWA doesn't recognize HiC options
  
  (Asked by: username_0 on 2020-10-12)
  
  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](https://phasegenomics.github.io/2019/09/19/hic-alignment-and-qc.html)), 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.
  
  **Tags:** bwa, hi-c
  
  > **Comments:**
  > **username_1**: You can use `conda` to install and test the desired version of `bwa` to test. This will not interfere with whatever version installed on the server.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-10-12. Score: 3
  
  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.
  
  
  ---
  
  