From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 18 Apr 2019 14:32:37 +0000 (+0100)
Subject: JAL-1793 basic help text for VCF option
X-Git-Tag: Release_2_11_0~17^2~9
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=58ecc1bd5b01acd8f8378980f369003da9db2ee9;p=jalview.git

JAL-1793 basic help text for VCF option
---

diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html
index b8445af..57ffa08 100755
--- a/help/html/menus/alwfile.html
+++ b/help/html/menus/alwfile.html
@@ -129,6 +129,13 @@
           features</a> or <a href="../features/annotationsFormat.html">alignment
           annotations</a>.
     </em></li>
+    <li><strong>Load VCF File<br>
+    </strong><em>Load VCF annotations from a plain text or tab-indexed file.
+    <br>This option is offered for nucleotide alignments, and requires at least one
+    sequence to have known genomic coordinates.
+    <br>Genomic coordinates are attached to entries retrieved from Ensembl.
+    <br>Support for VCF was added in Jalview 2.11.
+    </em></li>
     <li><strong>Close (Control W)</strong><br> <em>Close
         the alignment window. Make sure you have saved your alignment
         before you close - either as a Jalview project or by using the <strong>Save
diff --git a/help/html/releases.html b/help/html/releases.html
index b58cb31..a8fce60 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -63,6 +63,8 @@ li:before {
       <td align="left" valign="top">
         <ul>
           <li>
+            <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
+          <li>
             <!-- JAL-3141 -->Optional automatic backups when saving
             Jalview project or alignment files</li>
           <li>