text: user1770: I have problem with one my BAMs---it appears to have invalid read groups. 
  Normally when I have such a problem, I remove all the read groups from the BAM header as follows:
  samtools view -H your.bam | grep -v "^@RG" | samtools reheader - original.bam > new.bam
  
  and then I would execute AddOrReplaceReadGroups from Picard:
  http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups
  I have tried this, and there must still be reads with a read group in the optional tags RG:Z:. 
  How to do I definitively remove all read groups from a BAM, including all of the reads?
  
  user77: You might have to manually strip those auxiliary tags off:
  samtools view -h your.bam | grep -v "^@RG" | sed "s/\tRG:Z:[^\t]*//" | samtools view -bo your_fixed.bam -
  
  The sed bit is searching for the aux tag and removing everything up to the next tab.
  
original_text: 1770: <p>I have problem with one my BAMs---it appears to have invalid read groups. </p>
  
  <p>Normally when I have such a problem, I remove all the read groups from the BAM header as follows:</p>
  
  <pre><code>samtools view -H your.bam | grep -v "^@RG" | samtools reheader - original.bam &gt; new.bam
  </code></pre>
  
  <p>and then I would execute <code>AddOrReplaceReadGroups</code> from Picard:</p>
  
  <p><a href="http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups" rel="noreferrer">http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups</a></p>
  
  <p>I have tried this, and there must still be reads with a read group in the optional tags <code>RG:Z:</code>. </p>
  
  <p>How to do I definitively remove all read groups from a BAM, including all of the reads?</p>
   77: <p>You might have to manually strip those auxiliary tags off:</p>
  
  <pre><code>samtools view -h your.bam | grep -v "^@RG" | sed "s/\tRG:Z:[^\t]*//" | samtools view -bo your_fixed.bam -
  </code></pre>
  
  <p>The <code>sed</code> bit is searching for the aux tag and removing everything up to the next tab.</p>
  