diff --git a/docs/htdocs/info/docs/tools/vep/script/index.html b/docs/htdocs/info/docs/tools/vep/script/index.html
index 3ff40c28d..589251956 100644
--- a/docs/htdocs/info/docs/tools/vep/script/index.html
+++ b/docs/htdocs/info/docs/tools/vep/script/index.html
@@ -94,8 +94,10 @@ <h1 id="contents"><img src="/i/16/documentation.png"/> Documentation contents</h
                     <li><a href="vep_download.html#download">Download</a></li>
                     <li><a href="vep_download.html#new">What's new in release [[SPECIESDEFS::ENSEMBL_VERSION]]</a></li>
                     <li><a href="vep_download.html#installer">Installation</a></li>
+                    <li><a href="vep_download.html#macos">Using VEP in macOS</a></li>
                     <li><a href="vep_download.html#windows">Using VEP in Windows</a></li>
                     <li><a href="vep_download.html#docker">Docker</a></li>
+                    <li><a href="vep_download.html#singularity">Singularity</a></li>
                 </ul>
                 
                 <br />
@@ -148,7 +150,10 @@ <h1 id="contents"><img src="/i/16/documentation.png"/> Documentation contents</h
                 <img src="/i/16/user.png"/> <a href="vep_example.html" class="notext" style="font-size:16px;font-weight:bold">Examples & use cases</a>
                 <ul>
                     <li><a href="vep_example.html#examples">Example commands</a></li>
-                    <li><a href="vep_example.html#gnomade">gnomAD exomes and genomes</a></li>
+                    <li><a href="vep_example.html#gnomad">gnomAD</a></li>
+                    <li><a href="vep_example.html#gerp">Conservation scores</a></li>
+                    <li><a href="vep_example.html#dbNSFP">dbNSFP</a></li>
+                    <li><a href="vep_example.html#StructVar">Structural variants</a></li>
                     <li><a href="vep_example.html#citations">Citations and VEP users</a></li>
                 </ul>
             </div>
@@ -162,6 +167,8 @@ <h1 id="contents"><img src="/i/16/documentation.png"/> Documentation contents</h
                     <li><a href="vep_other.html#pick">Summarising annotation</a></li>
                     <li><a href="vep_other.html#hgvs">HGVS notations</a></li>
                     <li><a href="vep_other.html#refseq">RefSeq transcripts</a></li>
+                    <li><a href="vep_other.html#colocated">Colocated variants</a></li>
+                    <li><a href="vep_other.html#shifting">Normalising consequences</a></li>
                 </ul>
                 
                 <br />
diff --git a/docs/htdocs/info/docs/tools/vep/script/vep_example.html b/docs/htdocs/info/docs/tools/vep/script/vep_example.html
index a325aacf2..402740ebe 100644
--- a/docs/htdocs/info/docs/tools/vep/script/vep_example.html
+++ b/docs/htdocs/info/docs/tools/vep/script/vep_example.html
@@ -272,11 +272,69 @@ <h2 id="StructVar">Structural Variants</h2>
 
   <h4>Prediction process</h4>
   <ul>
-  <li> The INFO keys 'END' or 'SVLEN' are present, the proportion of any overlapping feature covered by the variant is calculated
-  <li> If the SVTYPE or ALT is 'DEL', the variant tested for feature ablation/ truncation
-  <li> If the SVTYPE or ALT is 'DUP', the variant tested for feature amplification
-  <li> If the SVTYPE or ALT is 'INS' or 'DUP', the variant tested for feature elongatation
-  <li> SVTYPE is used in preference to ALT to derive the variant type of an SV with 'CN*' alleles
+  <li> If the INFO keys <code>END</code> or <code>SVLEN</code> are present, the proportion of any overlapping feature covered by the variant is calculated</li>
+  <li> The alternative allele (or <code>SVTYPE</code> in older VCF files) defines the type of structural variant; some types of structural variants are tested for specific consequences:</li>
+
+  <table class="ss">
+    <tr>
+      <th>Structural variant type</th>
+      <th>Abbreviation</th>
+      <th>Specific consequences</th>
+    </tr>
+    <tr class="bg1">
+      <td>Insertion</td>
+      <td>INS</td>
+      <td>Feature elongation</td>
+    </tr>
+    <tr class="bg2">
+      <td>Deletion</td>
+      <td>DEL</td>
+      <td>Feature truncation</td>
+    </tr>
+    <tr class="bg1">
+      <td>Duplication</td>
+      <td>DUP</td>
+      <td>Feature amplification/elongation</td>
+    </tr>
+    <tr class="bg2">
+      <td>Inversion</td>
+      <td>INV</td>
+      <td><i>Not tested for any specific consequence</i></td>
+    </tr>
+    <tr class="bg1">
+      <td>Copy number variation</td>
+      <td>CNV</td>
+      <td>Feature amplification/elongation (if copy number is 2) or truncation (if copy number is 0)</td>
+    </tr>
+    <tr class="bg2">
+      <td>Breakpoint variant</td>
+      <td>BND</td>
+      <td>Feature truncation</td>
+    </tr>
+  </table>
+  </ul>
+
+  <h5> Insertions and deletions</h5>
+
+  <ul>
+    <li> Supports <a href="/info/docs/tools/vep/vep_formats.html#sv">mobile element insertions/deletions</a>, including ALU, HERV, LINE1 and SVA elements
+    <ul>
+      <li> Currently, mobile element variants are treated as any insertion/deletion
+    </ul>
+  </ul>
+
+  <h5> Breakpoint variants</h5>
+
+  <ul>
+    <li> Supports chromosome synonyms in breakends (such as <code>chr4</code> and <code>NC_000004.12</code>)
+    <li> Processes <a href="/info/docs/tools/vep/vep_formats.html#sv">single breakends and multiple, comma-separated alternative breakends</a>
+    <li> Consequences are reported for each breakend; for instance, for a VCF input like <code>1 7936271 . N N[12:58877476[,N[X:10932343[</code>, it will report the consequences for each of the 3 breakends:
+    <ul>
+      <li> <code>N[12:58877476[</code>: consequences for the first alternative breakend near chr12:58877476
+      <li> <code>N[X:10932343[</code>: consequences for the second alternative breakend near chrX:10932343
+      <li> <code>N.</code>: consequences for the reference breakend near chr1:7936271 (represented as detailed in the <a href="https://samtools.github.io/hts-specs/VCFv4.4.pdf" rel="external">VCF 4.4 specification, section 5.4.9: Single breakends</a>)
+    </ul>
+    <li> In case of specific breakends not overlaping any reported Ensembl features (such as transcripts and regulatory regions), that specific breakend will <b>NOT</b> be presented in VEP output.
   </ul>
 
   <h4> Reported overlaps</h4>
@@ -284,13 +342,27 @@ <h4> Reported overlaps</h4>
   <li> VEP calculates the length and proportion of each genomic feature overlapped by a structural variant
   <li> Use the <a href="vep_options.html#opt_overlaps">--overlaps</a> option to enable this when using VCF or tab format.
        (This is reported by default in standard VEP and JSON format.)
-  <li> The keys bp_overlap and percentage_overlap are used in JSON format and OverlapBP and OverlapPC in other formats.
+  <li> The keys <code>bp_overlap</code> and <code>percentage_overlap</code> are used in JSON format and <code>OverlapBP</code> and <code>OverlapPC</code> in other formats.
+  </ul>
+
+  <h4> Plugin support</h4>
+
+  <ul>
+    <li> <a href="vep_plugins.html#CADD">CADD plugin</a>
+    <li> <a href="vep_plugins.html#Conservation">Conservation plugin</a>
+    <li> <a href="vep_plugins.html#NearestGene">NearestGene plugin</a>
+    <li> <a href="vep_plugins.html#Phenotypes">Phenotypes plugin</a>
+    <li> <a href="vep_plugins.html#StructuralVariantOverlap">StructuralVariantOverlap plugin</a>: please note that all features of this plugin have been ported to <a href="vep_custom.html">--custom annotation</a>, with additional improvements
+    <li> <a href="vep_plugins.html#TSSDistance">TSSDistance plugin</a>
   </ul>
 
   <h4> Changing memory requirements</h4>
   <ul>
   <li> By default, VEP does not annotate variants larger than 10M. If you are using the command
   line tool, you can use the <a href="vep_options.html#opt_max_sv_size">--max_sv_size</a> option to modify this.
+    <ul>
+      <li> This limit is not associated with breakpoint variants: each breakend in a breakpoint variant is analysed by VEP as a single base (the alternative sequence is currently ignored).
+    </ul>
   <li>By default, variants are analysed in batches of 5000. Using the <a href="vep_options.html#opt_buffer_size">--buffer_size</a>
   option to reduce this can reduce memory requirements, especially if your data is sparse.
   A smaller buffer size is essential when annotating structural variants with regulatory data.
diff --git a/docs/htdocs/info/docs/tools/vep/vep_formats.html b/docs/htdocs/info/docs/tools/vep/vep_formats.html
index 869d55005..18a097e7a 100644
--- a/docs/htdocs/info/docs/tools/vep/vep_formats.html
+++ b/docs/htdocs/info/docs/tools/vep/vep_formats.html
@@ -268,63 +268,7 @@ <h3 id="complex_vcf"> Complex VCF entries </h3>
     behaviour. It is recommended to use the
     <a href="script/vep_options.html#opt_allele_number">--allele_number</a> flag to track
     the correspondence between alleles as input and how they appear in the output.</p>
-    
 
-    <br />
-    <hr />
-    <h3 id="sv"> Structural variant types</h3>
-    
-    <p>VEP can also call consequences on structural variants using the
-      following input formats:</p>
-    <ul>
-      <li><a href="#default">Default VEP input</a></li>
-      <li><a href="#region">REST-style regions</a></li>
-      <li> <a href="#id">Variant identifiers</a></li>
-      <li> <a href="#vcf">VCF</a></li>
-    </ul>
-  
-    <p> To recognise a variant as a structural variant, the allele string
-      (or <code>SVTYPE</code> in the INFO column of the VCF format) must be set
-      to one of the currently supported values: </p>
-    
-    <ul>
-        <li><b>INS</b> - insertion</li>
-        <li><b>DEL</b> - deletion</li>
-        <li><b>DUP</b> - duplication</li>
-        <li><b>TDUP</b> - tandem duplication</li>
-        <li><b>INV</b> - inversion</li>
-        <li><b>CNV</b> - copy number variation</li>
-        <ul>
-          <li>
-            The copy number value can be specified,
-            such as <kbd>&ltCN0&gt</kbd> or <kbd>&ltCN=4&gt</kbd>
-          </li>
-        </ul>
-        <li><b>BND</b> - breakend</li>
-        <ul>
-          <li>
-            In VCF, breakend replacements are inserted into the <code>ALT</code>
-            column and need to meet the
-            <a rel="external" href="http://samtools.github.io/hts-specs/">HTS specifications</a>,
-            such as <kbd>A[22:22893780[,A[X:10932343[</kbd>.
-          </li>
-        </ul>
-    </ul>
-    
-    <p> Examples of structural variants encoded in VCF format: </p>
-    
-    <pre class="code sh_sh">
-#CHROM  POS        ID   REF  ALT             QUAL  FILTER  INFO
-1       160283     dup  .    &lt;DUP&gt;           .     .       SVTYPE=DUP;END=471362
-1       1385015    del  .    &lt;DEL&gt;           .     .       SVTYPE=DEL;END=1387562
-1       7936271    bnd  N    N[12:58877476[  .     .       SVTYPE=BND</pre>
-    
-    <p> See the <a
-    rel="external" href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/VCF%20%28Variant%20Call%20Format%29%20version%204.0/encoding-structural-variants">VCF
-    definition document</a> for more detail on how to describe
-    structural variants in VCF format. </p>
-
-   
     <br />
     <hr />
     <h2 id="hgvs"> HGVS identifiers</h2>
@@ -459,6 +403,96 @@ <h2 id="region"> REST-style regions</h2>
 # structural variant: inversion
 21:25587759-25587769/INV</pre>
 
+<br />
+    <hr />
+    <h2 id="sv"> Structural variant types</h2>
+
+    <p>VEP can also call consequences on structural variants using the
+      following input formats:</p>
+    <ul>
+      <li><a href="#default">Default VEP input</a></li>
+      <li><a href="#region">REST-style regions</a></li>
+      <li> <a href="#id">Variant identifiers</a></li>
+      <li> <a href="#vcf">VCF</a></li>
+    </ul>
+
+    <p> To recognise a variant as a structural variant, the allele string
+      (or <code>SVTYPE</code> in the INFO column of the VCF format) must be set
+      to one of the currently supported values: </p>
+
+    <ul>
+        <li><b>INS</b> - insertion</li>
+        <ul>
+          <li><b>INS:ME</b> - insertion of mobile element</li>
+          <li><b>INS:ME:ALU</b> - insertion of ALU element</li>
+          <li><b>INS:ME:HERV</b> - insertion of HERV element</li>
+          <li><b>INS:ME:LINE1</b> - insertion of LINE1 element</li>
+          <li><b>INS:ME:SVA</b> - insertion of SVA element</li>
+        </ul>
+
+        <li><b>DEL</b> - deletion</li>
+        <ul>
+          <li><b>DEL:ME</b> - deletion of mobile element</li>
+          <li><b>DEL:ME:ALU</b> - deletion of ALU element</li>
+          <li><b>DEL:ME:HERV</b> - deletion of HERV element</li>
+          <li><b>DEL:ME:LINE1</b> - deletion of LINE1 element</li>
+          <li><b>DEL:ME:SVA</b> - deletion of SVA element</li>
+        </ul>
+
+        <li><b>DUP</b> - duplication</li>
+        <ul>
+          <li><b>DUP:TANDEM</b> - tandem duplication</li>
+          <li><b>TDUP</b> - tandem duplication</li>
+        </ul>
+        <li><b>INV</b> - inversion</li>
+
+        <li><b>CNV</b> - copy number variation</li>
+        <ul>
+          <li>
+            The copy number value can be specified like so:
+            <ul>
+              <li><kbd>CN0</kbd></li>
+              <li><kbd>CN=4</kbd></li>
+              <li><kbd>CN3,CN4,CN6</kbd></li>
+              <li><kbd>CN=0,CN=2,CN=4</kbd></li>
+            </ul>
+          </li>
+          <li><b>CNV:TR</b> - tandem repeats</li>
+          <ul>
+            <li> Requires <code>INFO</code> fields describing the tandem repeat, such as <code>RUS</code> and <code>RN</code> – check <a href="https://samtools.github.io/hts-specs/VCFv4.4.pdf" rel="external">VCF 4.4 specification, section 5.7</a>
+            <li> Currently, the <code>CIRUC</code> and <code>CIRB</code> <code>INFO</code> fields are ignored when calculating alternative alleles in tandem repeats
+          </ul>
+        </ul>
+
+        <li><b>BND</b> - chromosome breakpoints</li>
+        <ul>
+          <li> Breakpoint variants are composed by one or more breakends
+          <li>
+            In VCF, breakend replacements are inserted into the <code>ALT</code>
+            column and need to meet the
+            <a rel="external" href="http://samtools.github.io/hts-specs/">HTS specifications</a>,
+            such as <kbd>TG[12:58877476[</kbd>
+          </li>
+          <li>Single breakends can be specified in <code>ALT</code>, such as <kbd>T.</kbd> and <kbd>.G</kbd></li>
+          <li>Multiple, comma-separated alternative breakends can be specified in <code>ALT</code>, such as <kbd>A[22:22893780[,A[X:10932343[</kbd></li>
+        </ul>
+    </ul>
+
+    <p>More information on how VEP processes structural variants can be found <a href="script/vep_example.html#StructVar">here</a>.</p>
+
+    <h3> Examples of structural variants encoded in VCF format </h3>
+
+    <pre class="code sh_sh">
+#CHROM  POS        ID   REF  ALT             QUAL  FILTER  INFO
+1       160283     dup  .    &lt;DUP&gt;           .     .       SVTYPE=DUP;END=471362
+1       1385015    del  .    &lt;DEL&gt;           .     .       SVTYPE=DEL;END=1387562
+1       7936271    bnd  N    N[12:58877476[  .     .       SVTYPE=BND</pre>
+
+    <p> See the <a
+    rel="external" href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/VCF%20%28Variant%20Call%20Format%29%20version%204.0/encoding-structural-variants">VCF
+    definition document</a> for more detail on how to describe
+    structural variants in VCF format. </p>
+
     <!-- Output formats -->
     <br />
     <hr style="margin-bottom:0"/>