4f34ad1308512a42b91b2a164e8c73d40dc18135
gperez2
  Wed Jun 10 12:03:40 2026 -0700
Staging the Varaico release 3 tracks, removing test tracks, and adding Updated pennantIcon to the superTrack and Varaico tracks, refs #37658

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 96648ebf779..a1f5fa0f221 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -150,30 +150,31 @@
 group phenDis
 visibility hide
 color 0,100,0
 type bigBed 9 +
 release alpha
 mouseOverField trait
 bigDataUrl /gbdb/$D/bbi/phegeni.bb
 urls studyId=https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$$ geneId1=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D geneId2=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D analysisId=https://www.ncbi.nlm.nih.gov/projects/SNP/gViewer/gView.cgi?aid=$$ catalogId=https://www.ebi.ac.uk/gwas/search?query=$$
 
 track varsInPubs
 shortLabel Variants in Papers
 longLabel Genetic Variants mentioned in scientific publications
 superTrack on
 group phenDis
 type bed 3
+pennantIcon Updated red
 
         track mastermind
         shortLabel Mastermind Variants
         longLabel Genomenon Mastermind Variants extracted from full text publications
         visibility dense
         type bigBed 9 +
         urls url=$$
         bigDataUrl /gbdb/$D/bbi/mastermind.bb
         noScoreFilter on
         exonNumbers off
         mouseOver <b>Variant</b>: $name<br>  <b>Gene</b>: $gene<br> <b>Linkout</b>: <a href="$url" target="_blank">$_mouseOver</a><br> <b>Article count 1</b>: $mmcnt1<br> <b>Article count 2</b>: $mmcnt2<br> <b>Article count 3</b>: $mmcnt3
         itemRgb on
         filter.mmcnt1 0
         filter.mmcnt2 0
         filter.mmcnt3 0
@@ -227,87 +228,56 @@
         bigDataUrl /gbdb/$D/pubs2/pubtatorDbSnp.bb
         noScoreFilter on
         exonNumbers off
         itemRgb on
         parent varsInPubs pack
         urls pubmedIds="https://www.ncbi.nlm.nih.gov/pubmed/$$"
         mouseOver $name found in ${numPubmedIds} PubMed articles
         html varsInPubs
 
         track varaico
         shortLabel Varaico Variants
         longLabel Varaico Variants extracted from full text publications, titles, and abstracts
         visibility dense
         type bigBed 9 +
         bigDataUrl /gbdb/$D/bbi/varaico.bb
+        pennantIcon Updated red
         noScoreFilter on
         exonNumbers off
         # itemRgb on
         dataVersion release 3 (20260527)
         parent varsInPubs pack
         urls outlink="$$" selectedPmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" rgene="https://www.ncbi.nlm.nih.gov/nuccore/$$"
         mouseOver <b>$hgncSymbol $variantOrigStrs</b> in: $author ($journal, $year) - $title <br> <b>Number of publications:</b> $articlesCount <br> <b>Variant Effect:</b> $variantEffect
         html varaico.html
 
         track varaicoSuppl
         shortLabel Varaico Variants (suppl)
         longLabel Varaico Variants extracted from Supplementary Data
         visibility dense
         type bigBed 9 +
         bigDataUrl /gbdb/$D/bbi/varaicoSuppl.bb
+        pennantIcon Updated red
         noScoreFilter on
         exonNumbers off
         # itemRgb on
         dataVersion release 3 (20260527)
         parent varsInPubs pack
         urls outlink="$$" selectedPmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" rgene="https://www.ncbi.nlm.nih.gov/nuccore/$$"
         mouseOver <b>$hgncSymbol $variantOrigStrs</b> in: $author ($journal, $year) - $title <br> <b>Number of publications:</b> $articlesCount <br> <b>Variant Effect:</b> $variantEffect
         html varaico.html
 
-        track varaicoTest
-        shortLabel Varaico Variants Test
-        longLabel Varaico Variants Test extracted from full text publications, titles, and abstracts
-        visibility pack
-        type bigBed 9 +
-        bigDataUrl /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527/$D/normalized_variants.$D.bb
-        noScoreFilter on
-        exonNumbers off
-        # itemRgb on
-        dataVersion release 3 (20260527)
-        parent varsInPubs pack
-        urls outlink="$$" selectedPmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" rgene="https://www.ncbi.nlm.nih.gov/nuccore/$$"
-        mouseOver <b>$hgncSymbol $variantOrigStrs</b> in: $author ($journal, $year) - $title <br> <b>Number of publications:</b> $articlesCount <br> <b>Variant Effect:</b> $variantEffect
-        html varaico.html
-        release alpha
-
-        track varaicoSupplTest
-        shortLabel Varaico Variants Test (suppl)
-        longLabel Varaico Variants Test extracted from Supplementary Data
-        visibility pack
-        type bigBed 9 +
-        bigDataUrl /hive/users/jbirgmei/TRACK_VERSIONS/v5_20260527/$D/normalized_variants_supplements.$D.bb
-        noScoreFilter on
-        exonNumbers off
-        # itemRgb on
-        dataVersion release 3 (20260527)
-        parent varsInPubs pack
-        urls outlink="$$" selectedPmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" rgene="https://www.ncbi.nlm.nih.gov/nuccore/$$"
-        mouseOver <b>$hgncSymbol $variantOrigStrs</b> in: $author ($journal, $year) - $title <br> <b>Number of publications:</b> $articlesCount <br> <b>Variant Effect:</b> $variantEffect
-        html varaico.html
-        release alpha
-
-
 track caseControl
 compositeTrack on
 shortLabel Case Control
 longLabel Case Control Consortium
 group phenDis
 visibility hide
 type chromGraph
 minMax 0,15
 linesAt 5,10
 
     track cccTrendPvalBd
     parent caseControl
     shortLabel CCC Bipolar Dis
     longLabel Case Control Consortium Bipolar Disorder Trend -log10 P-value
     priority 1