<mapID target="overview" url="html/features/overview.html" />
<mapID target="overviewprefs" url="html/features/preferences.html#overview" />
+
+ <mapID target="importvcf" url="html/features/importvcf.html" />
</map>
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
- <tocitem text="Structure Chooser" target="pdbchooser"/>
- <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
+ <tocitem text="VCF Import" target="vcfimport"/>
+ <tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
+
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+ <tocitem text="Annotating from VCF" target="importvcf" />
<tocitem text="Viewing RNA structure" target="varna" />
<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
<tocitem text="RNA Helices coloring" target="colours.rnahelices" />
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Importing Variants from VCF</title>
+</head>
+<body>
+ <p>
+ <strong>Importing Genomic Variants from VCF</strong>
+ </p>
+
+ <p>Jalview can annotate nucleotide sequences associated with
+ genomic loci with features representing variants imported from VCF
+ files. This new feature in Jalview 2.11, is currently tuned to work
+ best with tab indexed VCF files produced by the GATK Variant
+ Annotation Pipeline (with or without annotation provided by the
+ Ensembl Variant Effect Predictor), but other sources of VCF files
+ should also work.</p>
+ <p>
+ If your sequences have genomic loci, then a <strong>Taxon
+ name</strong> and <strong>chromosome location</strong> should be shown in
+ the Sequence Details report and the Sequence ID tooltip (providing
+ you have enabled it via the submenu in the <em><strong>View</strong></em>
+ menu). Jalview matches the assembly information provided in the VCF
+ file to the taxon name, using an internal lookup table. If a match
+ is found, Jalview employs the Ensembl API's lift-over services to
+ locate your sequences' loci in the VCF file assembly's reference
+ frame. If all goes well, after loading a VCF, Jalview will report
+ the number of variants added as sequence features via the alignment
+ window's status bar. These are added by default when loci are
+ retrieved from Ensembl.
+ </p>
+ <p>
+ <strong>Working with variants from organisms other than
+ H.sapiens.</strong>
+ </p>
+ <ol>
+ <li>Look in your VCF file to identify keywords in the
+ ##reference header that define what species and assembly name the
+ VCF was generated against.</li>
+ <li>Look at ensembl.org to identify the species' short name,
+ and the assembly's unique.</li>
+ <li>Add mappings to the <strong>VCF_SPECIES</strong> and <strong>VCF_ASSEMBLY</strong>
+ properties in your .jalview_properties file. For example:<pre>
+VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans
+VCF_ASSEMBLY=assembly19=GRCh37,hs37=GRCh37</pre><br /> <br />These allow
+ annotations to be mapped from both Human 1000genomes VCF files and
+ C.elegans files.
+ </li>
+ </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
+ otherwise find it useful !</p>
+</body>
+</html>
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>
+ </strong><em><a href="../features/importvcf.html">Load VCF annotations</a> from a plain text, or indexed file (.csi,.tsi).
+ <br>Only available for nucleotide alignments, and requires at least one
+ sequence to have known genomic coordinates.</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
implementation that allows updates) used for Sequence Feature collections</li>
<li>
<li>
- <!-- JAL-2808,JAL-2069,JAL-2820 -->Sequence features can be filtered and
- shaded according to any associated attributes (e.g. variant
- attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)
- </li>
- <li>
+ <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
+ features can be filtered and shaded according to any
+ associated attributes (e.g. variant attributes from VCF
+ file, or key-value pairs imported from column 9 of GFF
+ file)
+ </li>
+ <li>
+ <!-- JAL-2879 -->Feature Attributes and shading schemes
+ stored and restored from Jalview Projects
+ </li>
+ <li>
<!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
recognise variant features
</li>
<!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
</li>
<li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
- <li>
- <!-- JAL-3225 -->Eclipse project configuration managed with
- gradle-eclipse
- </li>
- <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
- Atlassian Bamboo continuous integration for
- unattended Test Suite execution</li>
+ <li>
+ <!-- JAL-3225 -->Eclipse project configuration managed with
+ gradle-eclipse
+ </li>
+ <li>
+ <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian
+ Bamboo continuous integration for unattended Test Suite
+ execution
+ </li>
<li>
<!-- JAL-2864 -->Memory test suite to detect leaks in common
- operations</li>
- <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
- <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>
+ operations
+ </li>
+ <li>
+ <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+ issues resolved.
+ </li>
+ <li>
+ <!-- JAL-3248 -->Developer documentation migrated to
+ markdown (with HTML rendering)
+ </li>
+ <li>
+ <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+ </li>
+ <li>
+ <!-- JAL-3289 -->New URLs for publishing development
+ versions of Jalview
+ </li>
+ <li>
+ <li>
</ul>
</td>
<td align="left" valign="top">
<!-- JAL-2986 -->Sequence.findIndex returns wrong value when
sequence's End is greater than its length
</li>
- </ul> <em>New Known Defects</em>
+ <li><strong>Bugs fixed for Java 11 Support (not
+ yet on general release)</strong>
+ <ul>
+ <li>
+ <!-- JAL-3288 -->Menus work properly in split-screen
+ </li>
+ </ul></li>
+ </ul> <em>New Known Defects</em>
<ul>
<li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
</li>
<li>
<!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
</li>
- <li><strong>Java 11 Specific defects</strong>
+ <li>
+ <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
+ alignments with multiple views can close views unexpectedly
+ </li>
+ <li><strong>Java 11 Specific defects</strong>
<ul>
<li>
- <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
-
- </ul></li>
-
- </ul>
+ <!-- JAL-3235 -->Jalview Properties file is not sorted
+ alphabetically when saved
+ </li>
+ </ul>
+ </li>
+ </ul>
</td>
</tr>
<tr>
git://source.jalview.org / jalview.git / commitdiff