<p>New version of BCFTools (using call instead of view) doesn&#39;t produce VCF files with GQs in the FORMAT field.</p>

<p>Does anyone know how to get it in the new version (1.1)?</p>

<p>When you run bcftools call specify -f GQ to have it added to the output</p>

<pre>
 bcftools call -vmO z -f GQ</pre>
