More variation public doc updates

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

@@ -192,14 +192,6 @@ <h2 id="filter">Filtering results</h2>
                     <li><b>Allele, Feature type, Consequence, SIFT, PolyPhen and
                     Biotype</b> - for these columns, autocomplete will help you
                     fill in the value when you start typing</li>
-                    <li><p><b>SIFT and PolyPhen</b> - these columns can
-                    contain both text (e.g. a SIFT prediction) and a number
-                    (e.g. a frequency value). Ensembl VEP allows you to filter on
-                    either part of this.</p><p>For example, you may enter
-                    &quot;is&quot; and &quot;deleterious&quot; for SIFT to
-                    return deleterious predictions, or &quot;<&quot; and
-                    &quot;0.1&quot; to find results with a SIFT score less than
-                    0.1.</p></li>
                 </ul>
             </p>
         </div>

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

@@ -220,23 +220,18 @@ <h2 id="filter_write">Writing filters</h2>
 
     <pre class="code sh_sh"># find variants with AF > 0.1 in AFR or EUR but not EAS or SAS
 --filter "(AFR_AF > 0.1 or EUR_AF > 0.1) and (EAS_AF < 0.1 and SAS_AF < 0.1)"</pre>
-
-    <p> For fields that contain string and number components, filter_vep will
-    try and match the relevant part based on the operator in use. For example,
-    using <a href="vep_options.html#opt_sift">--sift b</a> in Ensembl VEP gives strings that look like
-    "tolerated(0.46)". This will give a match to either of the following
-    filters: </p>
-
-    <pre class="code sh_sh"># match string part
---filter "SIFT is tolerated"
-
-# match number part
---filter "SIFT < 0.5"</pre>
 
     <p> Note that for numeric fields, such as the *AF allele frequency fields, filter_vep does not consider the absence of a value for that field as equivalent to a 0 value.
     For example, if you wish to find rare variants by finding those where the allele frequency is less than 1% <b>or</b> absent, you should use the following:</p>
 
     <pre class="code sh_sh">--filter "AF < 0.01 or not AF"</pre>
+
+    <p> You can use regex to do pattern match. For example, using <a href="vep_options.html#opt_sift">--sift b</a> 
+        in Ensembl VEP gives field value that has both string and number and looks like "tolerated(0.46)". 
+        To match on the string part, you can do the following: </p>
+
+    <pre class="code sh_sh"># match string part
+--filter "SIFT match tolerated"</pre>
 
     <p> For the Consequence field it is possible to use the <a rel="external"
     href="http://www.sequenceontology.org/">Sequence Ontology</a> to match terms

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

@@ -219,7 +219,7 @@ <h2 id="run">Run Ensembl VEP</h2>
      <a href="vep_filter.html">filtering tool</a> to find only those that
     SIFT considers deleterious: </p>
 
-    <pre class="code sh_sh">./filter_vep -i variant_effect_output.txt -filter "SIFT is deleterious" | grep -v "##" | head -n5
+    <pre class="code sh_sh">./filter_vep -i variant_effect_output.txt -filter "SIFT match deleterious" | grep -v "##" | head -n5
 
 #Uploaded_variation  Location     Allele  Gene             Feature          ...  Extra
 rs2231495            22:17188416  C       ENSG00000093072  ENST00000262607  ...  SIFT=deleterious(0.05)
@@ -246,7 +246,7 @@ <h2 id="run">Run Ensembl VEP</h2>
     </p>
 
     <pre class="code sh_sh">./vep -i examples/homo_sapiens_GRCh38.vcf --cache --force_overwrite --sift b --canonical --symbol --tab --fields Uploaded_variation,SYMBOL,CANONICAL,SIFT -o STDOUT | \
-./filter_vep --filter "CANONICAL is YES and SIFT is deleterious"
+./filter_vep --filter "CANONICAL is YES and SIFT match deleterious"
 
 ...
 

ensembl/htdocs/info/genome/variation/prediction/protein_function.html

@@ -390,17 +390,19 @@ <h2 id="nsSNP_data_format">Prediction data format</h2>
 ("VAX" order, or "v" format if using the perl <i>pack</i> subroutine) unsigned short value. 
 The top three bits of this short 
 are used to encode the qualitative prediction, and the bottom ten bits are used to encode the prediction score. To decode the qualitative 
-prediction you should mask off all bits except the top three, and shift the resulting short
-right by 13 bits and treat this as an integer between zero and four. The corresponding prediction can then 
+prediction you should mask off all bits except the top two, and shift the resulting short
+right by 14 bits and treat this as an integer between zero and three. The corresponding prediction can then 
 be looked up in the table below. To decode the prediction score you should mask off the 
 top six bits and the resulting value can be treated as a number between zero and 1000, which 
 should be divided by 1000 to give a three decimal place score (casting to a floating point type
-if necessary). Bits 11-13 are not used, except to encode the "same as reference" dummy prediction 
+if necessary). Bits 11-14 are not used, except to encode the "same as reference" dummy prediction 
 <i>0xFFFF</i>.
 </p>
 <p>
   Note, for CADD prediction scores you do not need to divide by 1000 and use the value as is. For ESM1b scores
   you need to multiply by 100 and subtract by 50 <kbd>(value * 100 - 50)</kbd> after dividing by 1000.
+  Also, for AlphaMissense and ESM1b, the qualitative prediction is encoded using top three bits, and should be 
+  decoded accordingly.
 </p>
 
 <img src="/img/protein_function_encoding.png" style="width:500px;height:143px" alt="protein function encoding"/>

ensembl/htdocs/info/genome/variation/species/species_data_types.html

@@ -997,7 +997,7 @@ <h3>Species supported this way:</h3>
     <td style="text-align:center">-</td>
     <td style="text-align:center">-</td>
   </tr>
-  <tr style="vertical-align:middle">
+  <tr class="bg2" style="vertical-align:middle">
     <td>
       <div>
         <div style="float:left">
@@ -1173,6 +1173,7 @@ <h3>Species supported this way:</h3>
        </div>
     </td>
     <td style="text-align:right"><span class="vdoc_var_count vdoc_thousand" title="Over 81,000 variants">81 K</span></td>
+    <td style="text-align:center">-</td>
     <td style="text-align:center"><img src="/i/16/check.png" title="Data available" /></td>
     <td style="text-align:center"><img src="/i/16/check.png" title="Data available" /></td>
   </tr>