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+<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 id.</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>
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