ags.html"><code>check-tags</code> command</a>:</p>
<pre><code class="language-bash">$ modkit modbam check-tags ${bam} --head 1000
</code></pre>
<p>This command will return non-zero when you have invalid MM/ML <a href="https://samtools.github.io/hts-specs/SAMtags.pdf">SAMTags</a>.
You should expect to see an output similar to this:</p>
<pre><code class="language-text">&gt; checking tags on first 1000 reads
&gt; no errors
&gt; num PASS records: 1000 (100.00%)
&gt; num records: 1000
&gt; valid record tag heade