text: user6570: 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.
  
  user2776: 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
  
original_text: 6570: <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>
   2776: <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>
  