9d56da4ed4b38921527ecb425c79f7f809408345
lrnassar
  Fri Dec 13 14:08:41 2024 -0800
Adding colors to the REVEL and CADD tracks, refs #34732

diff --git src/hg/makeDb/trackDb/human/revel.html src/hg/makeDb/trackDb/human/revel.html
index e31cfbb..a2462bc 100644
--- src/hg/makeDb/trackDb/human/revel.html
+++ src/hg/makeDb/trackDb/human/revel.html
@@ -71,30 +71,57 @@
 genome, not on transcripts, and the choice of transcript is made by
 a variant calling software using a heuristic. In addition, clinically, in the
 field, some transcripts have been agreed-on as more relevant for a disease, e.g.
 because only certain transcripts may be expressed in the relevant tissue. So
 the choice of the most relevant transcript, and as such the REVEL score, may be
 a question of manual curation standards rather than a result of the variant itself.
 </p>
 </ul>
 
 <p>
 When using this track, zoom in until you can see every basepair at the
 top of the display. Otherwise, there are several nucleotides per pixel under 
 your mouse cursor and no score will be shown on the mouseover tooltip.
 </p>
 
+<p><b>Track colors</b></p>
+<p>
+This track is colored according to <a target="_blank" href="https://www.sciencedirect.com/science/article/pii/S000292972200461X">Table 2 in Vikas et al</a>. The colors represent the recommended ACMG/AMP score cutoffs.
+
+<table style="text-align: left;">
+  <thead>
+    <tr>
+      <th>Range</th>
+      <th>Classification</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>&ge; .773</td>
+      <td style="color: rgb(255,0,0);">Pathogenic</td>
+    </tr>
+    <tr>
+      <td>.772 - .184</td>
+      <td style="color: rgb(192,192,192);">Neutral</td>
+    </tr>
+    <tr>
+      <td>&le; .183</td>
+      <td style="color: rgb(80,166,230);">Benign</td>
+    </tr>
+  </tbody>
+</table>
+
 <p>For hg38, note that the data was converted from the hg19 data using the UCSC
 liftOver program, by the REVEL authors. This can lead to missing values or
 duplicated values. When a hg38 position is annotated with two scores due to the
 lifting, the authors removed all the scores for this position. They did the same when
 the reference allele has changed from hg19 to hg38.  Also, on hg38, the track has
 the "lifted" icon to indicate
 this. You can double-check if a nucleotide
 position is possibly affected by the lifting procedure by activating the track
 "Hg19 Mapping" under "Mapping and Sequencing".
 </p>
 
 <h2>Data access</h2>
 <p>
 REVEL scores are available at the 
 <a href="https://sites.google.com/site/revelgenomics/" target="_blank">