46a13fea0463e7ab3d3fe0f131476abbb7eca421
max
  Thu Sep 2 02:14:44 2021 -0700
Extending REVEL track docs after ML ticket, refs #28087

diff --git src/hg/makeDb/trackDb/human/revel.html src/hg/makeDb/trackDb/human/revel.html
index 3e5f21a..c32209b 100644
--- src/hg/makeDb/trackDb/human/revel.html
+++ src/hg/makeDb/trackDb/human/revel.html
@@ -4,30 +4,41 @@
 target="_blank">Rare Exome Variant Ensemble Learner</a> (REVEL) scores for predicting
 the deleteriousness of each nucleotide change in the genome.
 </p>
 
 <p>
 REVEL is an ensemble method for predicting the pathogenicity of missense variants 
 based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, 
 VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, 
 SiPhy, phyloP, and phastCons.  REVEL was trained using recently discovered pathogenic 
 and rare neutral missense variants, excluding those previously used to train its 
 constituent tools.  The REVEL score for an individual missense variant can range 
 from 0 to 1, with higher scores reflecting greater likelihood that the variant is 
 disease-causing. 
 </p>
 
+<p>Most authors of deleteriousness scores argue against using fixed cutoffs in
+diagnostics. But to give an idea of the meaning of the score value, the REVEL
+authors note: "For example, 75.4% of disease mutations but only 10.9% of
+neutral variants (and 12.4% of all ESVs) have a REVEL score above 0.5,
+corresponding to a sensitivity of 0.754 and specificity of 0.891. Selecting a
+more stringent REVEL score threshold of 0.75 would result in higher specificity
+but lower sensitivity, with 52.1% of disease mutations, 3.3% of neutral
+variants, and 4.1% of all ESVs being classified as pathogenic". (Figure S1 of
+the reference below)
+</p>
+
 <h2>Display Conventions and Configuration</h2>
 <p>
 There are four subtracks for this track: one for every nucleotide showing
 a score for the mutation represented by a mutation from the reference to that
 nucleotide. All subtracks show the REVEL ensemble score on mouseover, representing
 each of the possible &#126;9 billion SNVs in the genome. The score is an aggregation 
 of the outputs of the 13 tools.  
 </p>
 
 <p>
 For single nucleotide variants (SNV), at every
 genome position, there are three values per position, one for every possible
 nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing 
 the reference allele, e.g. A to A, is always set to zero, "0.0". REVEL only 
 takes into account amino acid changes, so a nucleotide change that results in no