Answers.Body: <p>Devon gives a practical answer using the great deepTools package. These should be the theoretical, lower level steps behind the plots:  </p>
  
  <ul>
  <li><p>Compute read depth at each genomic position, using for example <code>samtools mpileup</code> with appropriate flags to accept/reject reads. You get a table like:</p>
  
  <pre><code>Pos       Depth
  chr1:1    0
  chr1:2    10
  chr1:3    11
  ...
  chrX:100  10
  </code></pre></li>
  <li><p>For each unique value <em>x</em> in the <em>Depth</em> column count how many genomic positions have depth >= <em>x</em>. You can use Unix tools like <code>sort ... | uniq -c | awk ...</code> for this. You get a table like:</p>
  
  <pre><code>Depth   N bases with depth &gt;= x   % bases with depth &gt;= x
  0       (all genomic positions)   100 %
  1       1000                      90 %
  2       995                       85 %
  .
  .
  .
  N       2                         0.1 %                         
  </code></pre></li>
  <li><p>Now just plot column <code>Depth</code> (x) vs <code>% bases with depth &gt;= x</code> (y) with R or you favourite plotting tool.</p></li>
  </ul>
  
  <p>Did I get it right?</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-11T13:13:32.280Z
Answers.Text: yes, not sure bust does picar collectwgsmetrics do something similar?
Answers.UserDisplayName: novicebioinforesearcher
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-11T09:01:50.710Z
Answers.LastActivityDate: 2018-01-11T10:12:32.983Z
Answers.LastEditDate: 2018-01-11T10:12:32.983Z
Answers.UserDisplayName: dariober
Answers.Body: <p>The general steps are:</p>
  
  <ol>
  <li>Install <a href="http://deeptools.readthedocs.io/en/latest/content/installation.html" rel="noreferrer">deepTools</a></li>
  <li>Run <a href="http://deeptools.readthedocs.io/en/latest/content/tools/plotCoverage.html" rel="noreferrer">plotCoverage</a> on your BAM files</li>
  <li>Remove the left-most plot in photoshop/gimp/imagemagick</li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-11T00:36:35.663Z
Answers.Text: updated my question
Answers.UserDisplayName: novicebioinforesearcher
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-11T01:07:16.393Z
Answers.Text: Yes, I mean the left plot in the example, since it looks like you want % >= the coverage value on the X axis.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-11T00:24:27.057Z
Answers.LastActivityDate: 2018-01-11T00:24:27.057Z
Answers.UserDisplayName: Devon Ryan
Body: <p>Given a aligned bam file (wgs/bwa-mem) what steps do i need to perform to generate a plot as seen below (from this <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066621" rel="nofollow noreferrer">paper</a>):</p>
  
  <p><a href="https://i.sstatic.net/DQS8b.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/DQS8b.png" alt="enter image description here"></a></p>
  
  <p>We are trying to see how much of genome was covered using pacbio and illumina for cow.</p>
  
  <hr>
  
  <p>You mean remove this left plot?
  <a href="https://i.sstatic.net/JlgrX.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/JlgrX.png" alt="enter image description here"></a></p>
  
Tags: <wgs>
Title: Plot percentage of genome covered
ThreadText: # Plot percentage of genome covered
  
  (Asked by: username_0 on 2018-01-11)
  
  Given a aligned bam file (wgs/bwa-mem) what steps do i need to perform to generate a plot as seen below (from this [paper](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066621)):
  
  [![enter image description here](https://i.sstatic.net/DQS8b.png)](https://i.sstatic.net/DQS8b.png)
  
  We are trying to see how much of genome was covered using pacbio and illumina for cow.
  
  ---
  
  You mean remove this left plot?
  [![enter image description here](https://i.sstatic.net/JlgrX.png)](https://i.sstatic.net/JlgrX.png)
  
  **Tags:** wgs
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2018-01-11. Score: 5 | Accepted answer
  
  The general steps are:
  
  1. Install [deepTools](http://deeptools.readthedocs.io/en/latest/content/installation.html)
  2. Run [plotCoverage](http://deeptools.readthedocs.io/en/latest/content/tools/plotCoverage.html) on your BAM files
  3. Remove the left-most plot in photoshop/gimp/imagemagick
  
  > **Comments:**
  > **username_0**: updated my question  
  > **username_2**: Yes, I mean the left plot in the example, since it looks like you want % >= the coverage value on the X axis.  
  
  ---
  
  ### Answer by username_1 on 2018-01-11. Score: 1
  
  username_2 gives a practical answer using the great deepTools package. These should be the theoretical, lower level steps behind the plots:
  
  * Compute read depth at each genomic position, using for example `samtools mpileup` with appropriate flags to accept/reject reads. You get a table like:
  
    ```
    Pos       Depth
    chr1:1    0
    chr1:2    10
    chr1:3    11
    ...
    chrX:100  10
  
    ```
  * For each unique value *x* in the *Depth* column count how many genomic positions have depth >= *x*. You can use Unix tools like `sort ... | uniq -c | awk ...` for this. You get a table like:
  
    ```
    Depth   N bases with depth >= x   % bases with depth >= x
    0       (all genomic positions)   100 %
    1       1000                      90 %
    2       995                       85 %
    .
    .
    .
    N       2                         0.1 %                         
  
    ```
  * Now just plot column `Depth` (x) vs `% bases with depth >= x` (y) with R or you favourite plotting tool.
  
  Did I get it right?
  
  > **Comments:**
  > **username_0**: yes, not sure bust does picar collectwgsmetrics do something similar?  
  
  ---
  
  