<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>

CC BY-SA 3.0
2017-12-23T14:00:33.083Z
2017-12-23T14:00:33.083Z
Devon Ryan
<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>

<sam><samtools><reads><picard>
How to remove all BAM read groups from all reads (not just the header)?
# How to remove all BAM read groups from all reads (not just the header)?

(Asked by: username_0 on 2017-12-23)

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?

**Tags:** sam, samtools, reads, picard

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## 1 answers

### Answer by username_1 on 2017-12-23. Score: 7 | Accepted answer

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.


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