for more information.
</p>
<p>
+ <strong>Working with variants without CSQ fields</strong>
+ </p>
+ <p>
+ <a name="computepepvariants">Jalview 2.11.1's new virtual
+ features</a> mean that peptide sequences are no longer annotated
+ directly with protein missense variants. This makes it harder to
+ filter variants when they do not already include the CSQ field. You
+ can rescue the pre-2.11.1 functionality by:
+ </p>
+ <ol>
+ <li>Download the script at
+ https://www.jalview.org/examples/groovy/ComputePeptideVariants.groovy</li>
+ <li>Executing the script via the <a href="groovy.html">Groovy
+ Console</a> on a linked CDS/Protein view to create missense and
+ synonymous peptide variant features.
+ </li>
+ </ol>
+ <p>
<strong>Working with variants from organisms other than
H.sapiens.</strong>
</p>