Body: <p>I am trying to get base coverage information, and am using the <code>--PER_BASE_COVERAGE</code> output from Picard tools to get a text file of base level coverage. However, some of my targets are being grouped together. In the targets file, these are separated by one base as such:</p>
  
  <pre><code>12      12258595        12258695        +       TARGET1
  12      12258696        12258795        +       TARGET2
  12      12258796        12259791        +       TARGET3
  </code></pre>
  
  <p>However, when I look at my covg file, I see the following:</p>
  
  <pre><code>chr    pos    target   covg 
  12  12258595        TARGET1|TARGET2|TARGET3 510
  </code></pre>
  
  <p>Why would HSmetrics group these targets together, and how can I separate them?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-25T07:43:00.887Z
Comments.Text: Question is also asked on [biostars](https://www.biostars.org/p/365812/).
Comments.UserDisplayName: finswimmer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-25T09:34:32.547Z
Comments.Text: Hello @Blaze9, I don't understand your question. Would you maybe explain bit what are the targets? Are they read groups? (disclaimer, I am not a Picard tools user); I usually use samtools for this.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-25T16:14:08.780Z
Comments.Text: Hi @KamilSJaron, the targets are either tiling regions or exons/introns. I can checkout samtools to see if it provides better results. The per_target_coverage output does not combine the targets which is the weird part. Thanks!
Comments.UserDisplayName: Blaze9
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-25T17:42:01.620Z
Comments.Text: Ah, I see. Maybe you want to [edit] your question and add as many details as you can (such those you wrote in the comment) :-).
Comments.UserDisplayName: Kamil S Jaron
Tags: <coverage><picard>
Title: CollectHsMetrics base coverage output has overlapping targets
ThreadText: # CollectHsMetrics base coverage output has overlapping targets
  
  (Asked by: username_0 on 2019-02-25)
  
  I am trying to get base coverage information, and am using the `--PER_BASE_COVERAGE` output from Picard tools to get a text file of base level coverage. However, some of my targets are being grouped together. In the targets file, these are separated by one base as such:
  
  ```
  12      12258595        12258695        +       TARGET1
  12      12258696        12258795        +       TARGET2
  12      12258796        12259791        +       TARGET3
  
  ```
  
  However, when I look at my covg file, I see the following:
  
  ```
  chr    pos    target   covg 
  12  12258595        TARGET1|TARGET2|TARGET3 510
  
  ```
  
  Why would HSmetrics group these targets together, and how can I separate them?
  
  **Tags:** coverage, picard
  
  > **Comments:**
  > **username_1**: Question is also asked on [biostars](https://www.biostars.org/p/365812/).  
  > **username_2**: Hello @username_0, I don't understand your question. Would you maybe explain bit what are the targets? Are they read groups? (disclaimer, I am not a Picard tools user); I usually use samtools for this.  
  > **username_0**: Hi @username_2, the targets are either tiling regions or exons/introns. I can checkout samtools to see if it provides better results. The per_target_coverage output does not combine the targets which is the weird part. Thanks!  
  > **username_2**: Ah, I see. Maybe you want to [edit] your question and add as many details as you can (such those you wrote in the comment) :-).  
  
  ---
  
  ## 0 answers
  
  