00dbf34a4ecca1b801d643ff6baecca5737cd581
dschmelt
  Tue Sep 22 15:31:34 2020 -0700
Pushing COVID GWAS and LOVD tracks refs 25841, 26129

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 1178019..39f4a66 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -141,31 +141,32 @@
 filterValues.variant_class Amplification,Copy-Number Gain,Deletion,Duplication,Duplication/Trip
 filterValues.pathogenicity Benign,Likely Benign,Likely Pathogenic,Pathogenic,Uncertain,Unknown
 mergeSpannedItems on
 searchIndex name
 mouseOverField _mouseOver
 release alpha,beta
 
 searchTable decipher
 searchMethod exact
 searchType bigBed
 release alpha,beta
 
 track decipherSnvs
 shortLabel DECIPHER SNVs
 longLabel DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs)
-group phenDis
+group phenDisbigDataUrl /gbdb/$D/decipher/decipherCnv.bb
+
 visibility hide
 color 0,0,0
 type bed 4
 tableBrowser off decipherSnvsRaw
 prevExonText Left edge
 nextExonText Right edge
 html decipher
 
 track phegeni
 shortLabel PheGenI SNPs
 longLabel NCBI Phenotype-Genotype Integrator SNPs
 group phenDis
 visibility hide
 color 0,100,0
 type bigBed 9 +
@@ -3719,91 +3720,52 @@
         type bigBed 12 +
         release alpha
         bigDataUrl /gbdb/$D/bbi/cancerMutations/BRCA.bb
         urls case_id=https://portal.gdc.cancer.gov/cases/$$
         parent cancerMutations
 
 track lovdComp
 shortLabel LOVD Variants
 longLabel Leiden Open Variation Database Public Variants
 group phenDis
 visibility hide
 compositeTrack on
 type bigBed 4 +
 tableBrowser off lovdComp
 html lovdComp
-release alpha,beta
 
         track lovdShort
         shortLabel LOVD Variants < 50 bp
         longLabel Leiden Open Variation Database, short < 50 bp variants
         group phenDis
         visibility hide
         urls id="http://varcache.lovd.nl/redirect/$$"
         noScoreFilter on
         bigDataUrl /gbdb/$D/lovd/lovd.$D.short.bb
         parent lovdComp
-        release alpha,beta
 
         track lovdLong
         type bigBed 9 +
         shortLabel LOVD Variants >= 50 bp
         longLabel Leiden Open Variation Database Public Variants, long >= 50 bp variants
         group phenDis
         visibility hide
         urls id="http://varcache.lovd.nl/redirect/$$"
         noScoreFilter on
         bigDataUrl /gbdb/$D/lovd/lovd.$D.long.bb
         parent lovdComp
         mergeSpannedItems on
-        release alpha,beta
-
-track lovdComp
-shortLabel LOVD Variants
-longLabel Leiden Open Variation Database Public Variants
-group phenDis
-visibility hide
-compositeTrack on
-type bedDetail
-tableBrowser off lovdComp
-html lovdComp
-release public
-
-        track lovdShort
-        shortLabel LOVD Variants < 50bp
-        longLabel Leiden Open Variation Database, short < 50bp variants
-        group phenDis
-        visibility hide
-        type bedDetail 6
-        url http://varcache.lovd.nl/redirect/$$
-        urlLabel Link to LOVD:
-        noScoreFilter on
-        parent lovdComp
-        release public
-
-        track lovdLong
-        shortLabel LOVD Variants >= 50bp
-        longLabel Leiden Open Variation Database Public Variants, long >= 50bp variants
-        group phenDis
-        visibility hide
-        type bedDetail 6
-        url http://varcache.lovd.nl/redirect/$$
-        urlLabel Link to LOVD:
-        noScoreFilter on
-        parent lovdComp
-        release public
-
 
 track hgmd
 shortLabel HGMD Variants
 longLabel Human Gene Mutation Database Public Variants
 group phenDis
 visibility hide
 itemRgb on
 type bigBed 9 .
 url http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$P&accession=$p
 urlLabel Link to HGMD
 mouseOverField variantType
 tableBrowser off hgmd
 noScoreFilter on
 maxItems 1000
 
@@ -5504,16 +5466,16 @@
 track sgpGene override
 longLabel SGP Gene Predictions Using Mouse/$Organism Homology
 
 searchTable cnvDevDelayCase
 semiShortCircuit 1
 termRegex nssv[0-9]+
 searchType bed
 searchPriority 50
 
 searchTable cnvDevDelayControl
 semiShortCircuit 1
 termRegex nssv[0-9]+
 searchType bed
 searchPriority 50
 
-include covidHgiGwas.ra alpha,beta,public
+include covidHgiGwas.ra