06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/makeDb/trackDb/human/clinvar.html src/hg/makeDb/trackDb/human/clinvar.html
index c65bc19..fc409ca 100644
--- src/hg/makeDb/trackDb/human/clinvar.html
+++ src/hg/makeDb/trackDb/human/clinvar.html
@@ -76,61 +76,70 @@
 
 <p>
 Entries in the <b>ClinVar SNVs and ClinVar Interpretations tracks</b> are colored by <b>clinical 
 significance</b>:
 <ul>
  <li><b><font color="d20000">red for pathogenic</font></b></li>
  <li><b><font color="000088">dark blue for variant of uncertain significance</font></b></li>
  <li><B><font color="#00d200">green for benign</font></b></li>
  <li><B><font color="#888">dark grey for not provided</font></b></li>
  <li><B><font color="#8979D4">light blue for conflicting</font></b></li>
 </ul>
 </p>
 
 <p>
 The variants in the <b>ClinVar Interpretations track</b> are sorted by the variant 
-classification of each submission (P: Pathogenic, LP: Likely Pathogenic, VUS: Variant of 
-Unknown Significance, LB: Likely Benign, B: Benign, OTH: Others), the size of the bead represents 
+classification of each submission:
+<ul>
+ <li><b>P:</b> Pathogenic</li>
+ <li><b>LP:</b> Likely Pathogenic</li>
+ <li><b>VUS:</b> Variant of Unknown Significance</li>
+ <li><b>LB:</b> Likely Benign</li>
+ <li><b>B:</b> Benign</li>
+ <li><b>OTH:</b> Others</li>
+</ul>
+The size of the bead represents 
 the number of submissions at that genomic position. 
 Hovering on the track items shows the genomic variations which start at that position 
 and the number of individual submissions with that classification. The details page lists all
 rated submissions from ClinVar, with specific details to the interpretation of the clinical or 
 functional significance of each variant in relation to a condition. Interpretation is at 
 variant-level, not at case (or patient-specific) level.
 </p>
 
 <p>
 More information about using and understanding the ClinVar data can be found 
 <a target="_blank" href="https://www.ncbi.nlm.nih.gov/clinvar/docs/faq/">here</a>.
 </p>
 
 <p>
 For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a 
 mitochondrial genome "chrM" that was not the same as the one later used for most
 databases like ClinVar. As a result, we added the official mitochondrial genome
 in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other
 databases are shown on the mitochondrial genome called "chrMT". For full description
 of the issue of the mitochondrial genome in hg19, please see the 
 <a target=_blank href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/">README file</a> 
 on our download site. 
 </p>
 
 
 <h2>Data updates</h2>
 <p>ClinVar publishes a new release on the 
-<a href="https://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=ClinVarNews">first Thursday every month</a> 
-and this track is updated automatically at most six days 
+<a target="_blank"
+href="https://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=ClinVarNews">first Thursday every month</a>. 
+This track is then updated automatically at most six days 
 later. The exact date of our last update is shown when you click onto any variant. 
 You can find the previous versions of the track organized by month on our
 downloads server in the 
 <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/archive/clinvar/" target="_blank">archive</a>
 directory. To access one of these previous versions, paste the URL to one of
 the older files into our "Custom tracks" box.</p>
 
 <H2>Data access</H2>
 <p>
 The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>
 or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. The data can be
 accessed from scripts through our <a href="https://api.genome.ucsc.edu">API</a>, the track names are
 "clinVarMain and "clinVarCnv".
 
 <p>