Update docs related to GENCODE primary

docs/htdocs/info/docs/tools/vep/online/input.html

@@ -79,6 +79,11 @@ <h2 id="input">Data input</h2>
                   majority of users. GENCODE Basic includes all genes in the
                   GENCODE gene set, with a representative subset of the
                   transcripts (splice variants). </p>
+                  <p> GENCODE Primary is a new transcript subset which covers
+                  all human exons in a minimal set of transcripts. 
+                  This aims to enable annotation of all potential variant 
+                  consequences without duplication across multiple transcripts.
+                  </p>
                   <p>You can also select to use RefSeq transcripts from the <a
                   href="/info/docs/api/core/index.html#est">otherfeatures
                   database</a>; note though that these transcripts are simply
@@ -114,8 +119,7 @@ <h2 id="input">Data input</h2>
 
               <div class="ff-right vep_left_label vep_left_input"><div><b>Or provide file URL:</b></div></div><div class="ff-right"><input type="text" size="30" class="ftext optional url _url"></div>
             </div>
-
-            <div class="form-field _stt_rfq" style="display: block;"><label class="ff-label"><span class="_ht ht">Transcript database to use</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="radio" class="_stt" checked="checked"><label class="ff-checklist-label">Ensembl<span style="display: inline;">/GENCODE</span> transcripts</label></p><p class="ff-checklist" style="display: block;"><input type="radio" class="_stt"><label class="ff-checklist-label">Ensembl/GENCODE basic transcripts</label></p><p class="ff-checklist"><input class="_stt" type="radio"><label class="ff-checklist-label">RefSeq transcripts</label></p><p class="ff-checklist"><input class="_stt" type="radio"><label class="ff-checklist-label">Ensembl<span style="display: inline;">/GENCODE</span> and RefSeq transcripts</label></p></div></div></fieldset></form>
+            <div class="form-field _stt_rfq" style="display: block;"><label class="ff-label"><span class="_ht ht">Transcript database to use</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="radio" class="_stt" checked="checked"><label class="ff-checklist-label">Ensembl<span style="display: inline;">/GENCODE</span> transcripts</label></p><p class="ff-checklist" style="display: block;"><input type="radio" class="_stt"><label class="ff-checklist-label">Ensembl/GENCODE basic transcripts</label></p><p class="ff-checklist" style="display: block;"><input type="radio" class="_stt"><label class="ff-checklist-label">Ensembl/GENCODE primary transcripts</label><p class="ff-checklist"><input class="_stt" type="radio"><label class="ff-checklist-label">RefSeq transcripts</label></p><p class="ff-checklist"><input class="_stt" type="radio"><label class="ff-checklist-label">Ensembl<span style="display: inline;">/GENCODE</span> and RefSeq transcripts</label></p></div></div></fieldset></form>
       </div>
     </div>
 </div>
@@ -511,7 +515,7 @@ <h2>Transcript annotation</h2>
               <div class="form-field" style="display: block;"><label class="ff-label">Transcript support level:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox" checked="checked"></p></div></div>
               <div class="form-field" style="display: block;"><label class="ff-label"><span class="_ht ht">APPRIS</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox" checked="checked"></p></div></div>
               <div class="form-field" style="display: block;"><label class="ff-label"><span class="_ht ht">MANE</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox" checked="checked"></p></div></div>
-              <div class="_stt_merged form-field _stt_core _stt_gencode_basic" style="display: block;"><label class="ff-label">Identify canonical transcripts:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox"></p></div></div>
+              <div class="_stt_merged form-field _stt_core _stt_gencode_basic _stt_gencode_primary " style="display: block;"><label class="ff-label">Identify canonical transcripts:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox"></p></div></div>
               <div class="form-field"><label class="ff-label"><span class="ht _ht">Upstream/Downstream distance (bp)</span>:</label><div class="ff-right"><input value="5000" class="optional _string ftext" type="text"></div></div>
               <div class="form-field"><label class="ff-label"><span class="_ht ht">miRNA structure</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox" ></p></div></div>
               <div class="form-field"><label class="ff-label"><span class="ht _ht">NMD</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox" class="_stt plugin_enable"></p></div></div>
@@ -521,14 +525,14 @@ <h2>Transcript annotation</h2>
 
             <fieldset>
               <h2>Protein annotation</h2>
-              <div class="_stt_merged form-field _stt_core _stt_gencode_basic" style="display: block;"><label class="ff-label"><span class="ht _ht">Protein matches</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox"></p></div></div>
+              <div class="_stt_merged form-field _stt_core _stt_gencode_basic _stt_gencode_primary" style="display: block;"><label class="ff-label"><span class="ht _ht">Protein matches</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox"></p></div></div>
               <div class="_stt_Mus_musculus form-field _stt_Homo_sapiens" style="display: block;"><label class="ff-label"><span class="_ht ht">mutfunc</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="radio" checked="checked" class="_stt plugin_enable"><label class="ff-checklist-label">Disabled</label></p><p class="ff-checklist"><input type="radio" class="plugin_enable _stt"><label class="ff-checklist-label">Enabled</label></p></div></div>
             </fieldset>
 
             <fieldset>
               <h2>Functional effect</h2>
               <div class="_stt_Mus_musculus form-field _stt_Homo_sapiens" style="display: block;"><label class="ff-label"><span class="_ht ht">IntAct</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="radio" checked="checked" class="_stt plugin_enable"><label class="ff-checklist-label">Disabled</label></p><p class="ff-checklist"><input type="radio" class="plugin_enable _stt"><label class="ff-checklist-label">Enabled</label></p></div></div>
-              <div class="_stt_merged form-field _stt_core _stt_gencode_basic" style="display: block;"><label class="ff-label"><span class="ht _ht">MaveDB</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox"></p></div></div>
+              <div class="_stt_merged form-field _stt_core _stt_gencode_basic _stt_gencode_primary" style="display: block;"><label class="ff-label"><span class="ht _ht">MaveDB</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox"></p></div></div>
             </fieldset>
 
             <fieldset>

docs/htdocs/info/docs/tools/vep/script/vep_options.html

@@ -490,6 +490,7 @@ <h2 id="cacheopt">Cache options</h2>
       <td>REFSEQ_MATCH, BAM_EDIT</td>
       <td>
         <div style="padding:2px 0px"><a href="#opt_gencode_basic">--gencode_basic</a></div>
+        <div style="padding:2px 0px"><a href="#opt_gencode_primary">--gencode_primary</a></div>
         <div style="padding:2px 0px"><a href="#opt_merged">--merged</a></div>
       </td>
     </tr>
@@ -1698,6 +1699,26 @@ <h2 id="filt">Filtering and QC options</h2>
       </td>
       <td>&nbsp;</td>
       <td>
+        <div style="padding:2px 0px"><a href="#opt_gencode_primary">--gencode_primary</a></div>
+        <div style="padding:2px 0px"><a href="#opt_refseq">--refseq</a></div>
+      </td>
+    </tr>
+    <tr id="opt_gencode_primary">
+      <td><pre>--gencode_primary</pre></td>
+      <td>&nbsp;</td>
+      <td>
+        Limit your analysis to transcripts belonging to the GENCODE
+        primary set. This set covers all human exons in a minimal set of transcripts. <i>Not used by default</i>
+        <div class="info" style="max-width:350px;margin:5px 0px 5px 10px">
+          <h3>Note</h3>
+          <div class="message-pad" style="padding:5px 10px;background-color:#FFF">
+            Only available for human on the GRCh38 assembly
+          </div>
+        </div>
+      </td>
+      <td>&nbsp;</td>
+      <td>
+        <div style="padding:2px 0px"><a href="#opt_gencode_basic">--gencode_basic</a></div>
         <div style="padding:2px 0px"><a href="#opt_refseq">--refseq</a></div>
       </td>
     </tr>
@@ -1995,6 +2016,21 @@ <h3>Note</h3>
         <div style="padding:2px 0px"><a href="#opt_vcf">--vcf</a></div>
       </td>
     </tr>
+    <tr id="opt_flag_gencode_primary">
+      <td><pre>--flag_gencode_primary</pre></td>
+      <td>&nbsp;</td>
+      <td>
+        Flags transcripts as GENCODE primary using a boolean value. <i>Not used by default</i>
+        <div class="info" style="max-width:350px;margin:5px 0px 5px 10px">
+          <h3>Note</h3>
+          <div class="message-pad" style="padding:5px 10px;background-color:#FFF">
+            Only available for human on the GRCh38 assembly
+          </div>
+        </div>
+      </td>
+      <td>GENCODE_PRIMARY</td>
+      <td>&nbsp;</td>
+    </tr>
     <tr id="opt_filter_common">
       <td><pre>--filter_common</pre></td>
       <td>&nbsp;</td>

docs/htdocs/info/docs/tools/vep/vep_formats.html

@@ -612,6 +612,7 @@ <h3 style="margin:20px 0px 30px">Other output fields:</h3>
         <li><b>BIOTYPE</b> - Biotype of transcript or regulatory feature</li>
         <li><b>APPRIS</b> - Annotates alternatively spliced transcripts as primary or alternate based on a range of computational methods. NB: not available for GRCh37</li>
         <li><b>TSL</b> - Transcript support level. NB: not available for GRCh37</li>
+        <li><b>GENCODE_PRIMARY</b> - Reports if transcript belongs to GENCODE primary subset</li>
         <li><b>PUBMED</b> - Pubmed ID(s) of publications that cite existing variant</li>
         <li><b>SOMATIC</b> - Somatic status of existing variant(s); multiple values correspond to multiple values in the Existing_variation field</li>
         <li><b>PHENO</b> - Indicates if existing variant is associated with a phenotype, disease or trait; multiple values correspond to multiple values in the Existing_variation field</li>