Answers.Body: <p>Pilon will not consider fragments that are not proper pairs if the <code>--frags</code> option is used to pass the alignment <code>.bam</code> file. The reads mapped in the above IGV screenshot are unpaired.</p>
  
  <p>Instead, if you want Pilon to consider <em>all</em> reads that map as legitimate and usable for correction, pass the <code>.bam</code> file with the <code>--unpaired</code> option instead.</p>
  
  <p>To above corrected example would be:</p>
  
  <pre><code>java -Xmx100G -jar {params.pilon}\
    --genome {input.ref}\
    --unpaired {input.bam}\
    --output {params.outname}\
    --changes --fix all,amb,breaks,bases\
    --threads {threads}\
    --mindepth 1
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-02T17:26:42.623Z
Answers.LastActivityDate: 2018-08-02T17:26:42.623Z
Answers.UserDisplayName: conchoecia
Body: <p>I have mapped some reads to a reference and want to change SNPs in the reference to SNPs found in the reads, even at low coverage. For example, here is a screenshot of one reference in IGV that I would like to correct. </p>
  
  <p><a href="https://i.sstatic.net/zlUhX.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/zlUhX.png" alt="enter image description here"></a></p>
  
  <p>When I use pilon to try to correct the reference, however, no bases are ever changed, even if using the option <code>--mindepth 1</code>.</p>
  
  <p>Here is the call that I am using:</p>
  
  <pre><code>java -Xmx100G -jar {params.pilon}\
    --genome {input.ref}\
    --frags {input.bam}\
    --output {params.outname}\
    --changes --fix all,amb,breaks,bases\
    --threads {threads}\
    --mindepth 1
  </code></pre>
  
  <p>How can I use even low-coverage information to correct my reference?</p>
  
Tags: <sam><reference-genome><read-correction>
Title: How to force pilon to correct a reference with low coverage mapped reads?
ThreadText: # How to force pilon to correct a reference with low coverage mapped reads?
  
  (Asked by: username_0 on 2018-08-02)
  
  I have mapped some reads to a reference and want to change SNPs in the reference to SNPs found in the reads, even at low coverage. For example, here is a screenshot of one reference in IGV that I would like to correct.
  
  [![enter image description here](https://i.sstatic.net/zlUhX.png)](https://i.sstatic.net/zlUhX.png)
  
  When I use pilon to try to correct the reference, however, no bases are ever changed, even if using the option `--mindepth 1`.
  
  Here is the call that I am using:
  
  ```
  java -Xmx100G -jar {params.pilon}\
    --genome {input.ref}\
    --frags {input.bam}\
    --output {params.outname}\
    --changes --fix all,amb,breaks,bases\
    --threads {threads}\
    --mindepth 1
  
  ```
  
  How can I use even low-coverage information to correct my reference?
  
  **Tags:** sam, reference-genome, read-correction
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-08-02. Score: 1 | Accepted answer
  
  Pilon will not consider fragments that are not proper pairs if the `--frags` option is used to pass the alignment `.bam` file. The reads mapped in the above IGV screenshot are unpaired.
  
  Instead, if you want Pilon to consider *all* reads that map as legitimate and usable for correction, pass the `.bam` file with the `--unpaired` option instead.
  
  To above corrected example would be:
  
  ```
  java -Xmx100G -jar {params.pilon}\
    --genome {input.ref}\
    --unpaired {input.bam}\
    --output {params.outname}\
    --changes --fix all,amb,breaks,bases\
    --threads {threads}\
    --mindepth 1
  
  ```
  
  
  ---
  
  