<p>Hi all,</p>

<p>Can you tell me what's the meaning of <strong>@RG</strong> / <strong>group</strong> in the <strong>SAM</strong> format. Can I consider it as the very same thing as '<strong>Sample-name</strong>' ?</p>

<p>Is there a case where one could find more than one <strong>@RG</strong> tag in a <strong>BAM</strong> file ?</p>

<p>Can <strong>mpileup</strong> (or another software) use this <strong>@RG</strong> flag to put more than one sample column in a <strong>VCF</strong> file.</p>

<p>If yes, what does it mean for the <strong>QUAL</strong> column ?</p>

<p>If no, under which condition can we find more than one sample column in a VCF ?</p>

<p>Thanks,</p>

<p>Pierre</p>

<p>For Illumina reads, RG typically groups reads from a lane. GATK requires/assumes such a use in several components. At least one should not put reads from multiple libraries in the same RG.</p>

<p>When reading the input BAMs, <a href='http://samtools.sourceforge.net/'>samtools</a> tries to group reads based on their @RG-SM tag. If there are no @RG lines, it implicitly inserts the following line into the header:</p>

<pre><code>@RG ID:filename SM:filename
</code></pre>

<p>The VCF spec is very clear about the definition of QUAL: the probability of there being no SNPs in any samples.</p>
