JAL-4090 smaller associate PDB file panel image in docs

[jalview.git] / help / help / html / features / importvcf.html

diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html
index 511ff2e..ffc9fa7 100755 (executable)
--- a/help/help/html/features/importvcf.html
+++ b/help/help/html/features/importvcf.html
@@ -72,6 +72,24 @@
     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>
@@ -91,7 +109,7 @@ VCF_ASSEMBLY=assembly19=GRCh37,hs37=GRCh37</pre><br /> <br />These allow
   </ol>
   <strong>Work in Progress!</strong>
   <p>VCF support in Jalview is under active development. Please get
-    in touch via our mailing list if you have any questions, problems or
+    in touch via our discussion forum if you have any questions, problems or
     otherwise find it useful !</p>
 </body>
 </html>