<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>

CC BY-SA 4.0
2019-02-25T07:43:00.887Z
Question is also asked on [biostars](https://www.biostars.org/p/365812/).
finswimmer
CC BY-SA 4.0
2019-02-25T09:34:32.547Z
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.
Kamil S Jaron
CC BY-SA 4.0
2019-02-25T16:14:08.780Z
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!
Blaze9
CC BY-SA 4.0
2019-02-25T17:42:01.620Z
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) :-).
Kamil S Jaron
<coverage><picard>
CollectHsMetrics base coverage output has overlapping targets
# 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 @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.  
> **username_0**: 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!  
> **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

