1cc7074f2d1b95838058636db75560afad9abc02
dschmelt
  Thu Nov 12 15:42:03 2020 -0800
Making changes to release COVID Risk var track #26351

diff --git src/hg/makeDb/trackDb/human/covidMuts.html src/hg/makeDb/trackDb/human/covidMuts.html
index fe051f7..d47d628 100644
--- src/hg/makeDb/trackDb/human/covidMuts.html
+++ src/hg/makeDb/trackDb/human/covidMuts.html
@@ -19,82 +19,82 @@
 
 <h2>Display Conventions</h2>
 <p>
 Only eight genes and few variants are contained in this track. Use the links in the table to
 browse the gene of interest:
 </p>
 
 <table class="stdTbl">
   <tr>
     <th>Gene Name</th>
     <th>Human GRCh37/hg19 Assembly</th>
     <th>Human GRCh38/hg38 Assembly</th>
   </tr>
   <tr>
    <td>TLR3</td>
-    <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr4:186990309-187006252">
+    <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr4:186990309-187006252">
 chr4:186990309-187006252</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr4:186069152-186088069">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr4:186069152-186088069">
 chr4:186069152-186088069</a></td>
   </tr>
   <tr>
     <td>IRF7</td>
-    <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr11:612555-615999">
+    <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr11:612555-615999">
 chr11:612555-615999</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr11:612591-615970">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr11:612591-615970">
 chr11:612591-615970</a></td>
   </tr>
   <tr>
     <td>UNC93B1</td>
-    <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr11:67758575-67771593">
+    <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr11:67758575-67771593">
 chr11:67758575-67771593</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr11:67991100-68004097">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr11:67991100-68004097">
 chr11:67991100-68004097</a></td>
   </tr>
   <tr>
     <td>TBK1</td>
-    <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr12:64845840-64895899">
+    <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr12:64845840-64895899">
 chr12:64845840-64895899</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr12:64452120-64502114">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr12:64452120-64502114">
 chr12:64452120-64502114</a></td>
   </tr>
   <tr>
     <td>TICAM1</td>
-    <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr19:4815936-4831754">
+    <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr19:4815936-4831754">
 chr19:4815936-4831754</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr19:4815932-4831704">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr19:4815932-4831704">
 chr19:4815932-4831704</a></td>
   </tr>
   <tr>
     <td>IRF3</td>
-    <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr19:50162826-50169132">
+    <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr19:50162826-50169132">
 chr19:50162826-50169132</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr19:49659570-49665875">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr19:49659570-49665875">
 chr19:49659570-49665875</a></td>
   </tr>
   <tr>
     <td>IFNAR1</td>
-   <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr21:34697214-34732128">
+   <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr21:34697214-34732128">
 chr21:34697214-34732128</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr21:33324970-33359864">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr21:33324970-33359864">
 chr21:33324970-33359864</a></td>
   </tr>
   <tr>
     <td>IFNAR2</td>
-    <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr21:34602231-34636820">
+    <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr21:34602231-34636820">
 chr21:34602231-34636820</a></td>
-    <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr21:33229974-33264525">
+    <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr21:33229974-33264525">
 chr21:33229974-33264525</a></td>
   </tr>
 </table>
 
 <h2>Methods</h2>
 <p>
 This track uses variant calls in autosomal IFN-related genes from whole exome and genome data 
 with a MAF lower than 0.001 (gnomAD v2.1.1) and experimental demonstration of loss-of-function.
 The patient population studied consisted of 659 patients with life-threatening COVID-19 pneumonia 
 relative to 534 subjects with asymptomatic or benign infection of varying ethnicities. 
 Variants underlying autosomal-recessive or autosomal-dominant deficiencies were identified in 
 23 patients (3.5%) 17 to 77 years of age.
 The proportion of individuals carrying at least one variant was compared between severe cases 
 and control cases by means of logistic regression with the likelihood ratio test.
 Principal Component Analysis (PCA) was conducted with Plink v1.9 software on whole exome and