Answers.Body: <p>This was answered by the OP -- it was a bug that has been fixed in a subsequent release, 4.1.5.0. See the release notes here: <a href="https://github.com/broadinstitute/gatk/releases/tag/4.1.5.0" rel="nofollow noreferrer">https://github.com/broadinstitute/gatk/releases/tag/4.1.5.0</a></p>
  
  <blockquote>
    <p>Made callable sites a Long to avoid integer overflow (#6303)</p>
  </blockquote>
  
  <p>Issue ticket: <a href="https://github.com/broadinstitute/gatk/issues/6302" rel="nofollow noreferrer">https://github.com/broadinstitute/gatk/issues/6302</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-08T10:13:28.963Z
Answers.Text: Hey ya, this could be a useful answer if you would provide some details, like the version where the bug is fixed and a link to the changelog. Right now it provides nothing than what OP wrote.
Answers.UserDisplayName: Kamil S Jaron
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-08T14:43:50.163Z
Answers.Text: Sure; done. I was just looking to not have it show up as unanswered anymore since the problem was effectively solved. But I get your point.
Answers.UserDisplayName: Geraldine_VdAuwera
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-07T03:12:11.520Z
Answers.LastActivityDate: 2020-04-08T14:42:48.793Z
Answers.LastEditDate: 2020-04-08T14:42:48.793Z
Answers.UserDisplayName: Geraldine_VdAuwera
Body: <p>I have adapted my pipeline to the new filtering strategies implemented in gatk 4.1.4.0 and while looking at its output I noticed that the stat file generated by mutect2 has a negative number:</p>
  
  <pre><code>callable -1.538687311E9
  </code></pre>
  
  <p>I did not find the documentation about this file content but in the gatk forum it is mentioned that is should represent the number of bases above a certain coverage (10 by default). 
  This happened for a WGS sample, while for WES I obtain a more sensible value (well, at least positive and integer, even if maybe a tad high):</p>
  
  <pre><code>callable        8.6884303E7
  </code></pre>
  
  <p>Has this happened to anyone else?
  I compared the resulting calls obtained for the WGS with a previous version of mutect2 and they are comparable-ish (98% of the new "ones" are in common with the "old" ones), but I am still worried that something fishy is happening, expecially considering that the filtering step of the pipeline uses this stats file.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-06T09:05:31.737Z
Comments.Text: quick followup: seems to be a bug due to an integer overflow (yay Java!), GATK developers have fixed it and I'm trying it out.
Comments.UserDisplayName: vodka
Tags: <wgs><gatk>
Title: GATK 4.1.4.0 Mutect stats output
ThreadText: # GATK 4.1.4.0 Mutect stats output
  
  (Asked by: username_0 on 2019-11-28)
  
  I have adapted my pipeline to the new filtering strategies implemented in gatk 4.1.4.0 and while looking at its output I noticed that the stat file generated by mutect2 has a negative number:
  
  ```
  callable -1.538687311E9
  
  ```
  
  I did not find the documentation about this file content but in the gatk forum it is mentioned that is should represent the number of bases above a certain coverage (10 by default).
  This happened for a WGS sample, while for WES I obtain a more sensible value (well, at least positive and integer, even if maybe a tad high):
  
  ```
  callable        8.6884303E7
  
  ```
  
  Has this happened to anyone else?
  I compared the resulting calls obtained for the WGS with a previous version of mutect2 and they are comparable-ish (98% of the new "ones" are in common with the "old" ones), but I am still worried that something fishy is happening, expecially considering that the filtering step of the pipeline uses this stats file.
  
  **Tags:** wgs, gatk
  
  > **Comments:**
  > **username_0**: quick followup: seems to be a bug due to an integer overflow (yay Java!), GATK developers have fixed it and I'm trying it out.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-04-07. Score: 1
  
  This was answered by the OP -- it was a bug that has been fixed in a subsequent release, 4.1.5.0. See the release notes here: <https://github.com/broadinstitute/gatk/releases/tag/4.1.5.0>
  
  > Made callable sites a Long to avoid integer overflow (#6303)
  
  Issue ticket: <https://github.com/broadinstitute/gatk/issues/6302>
  
  > **Comments:**
  > **username_2**: Hey ya, this could be a useful answer if you would provide some details, like the version where the bug is fixed and a link to the changelog. Right now it provides nothing than what OP wrote.  
  > **username_1**: Sure; done. I was just looking to not have it show up as unanswered anymore since the problem was effectively solved. But I get your point.  
  
  ---
  
  