d93d7b14a11b7c22b2275df5c8db88f9232efeb7
kate
  Thu Aug 27 11:00:26 2020 -0700
First cut COVID GWAS track. refs #26129

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 76f60c4..5d4a70b 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -9,32 +9,32 @@
 include trackDb.nt.ra
 
 # Denisova tracks
 include trackDb.denisova.ra
 
 # Genome variants aka pgSnp aka personal genomes
 include trackDb.pgSnp.ra
 
 # Genotype Tissue Expresssion (GTEx)
 include trackDb.gtex.ra
 
 # GeneHancer from Weizmann labs
 include trackDb.geneHancer.ra
 
 # NCBI ClinVar
-include trackDb.clinvar.ra public
-include trackDb.clinvarTest.ra alpha,beta
+include trackDb.clinvar.ra public,beta
+include trackDb.clinvarTest.ra alpha
 
 # NCBI dbVar
 include trackDb.dbVar.ra
 
 # ClinGen
 include trackDb.clinGen.ra alpha
 
 # Genome In a Bottle
 include trackDb.giab.ra alpha
 
 track cytoBandIdeo
 shortLabel Chromosome Band (Ideogram)
 longLabel Chromosome Bands Localized by FISH Mapping Clones (for Ideogram)
 group map
 visibility dense
@@ -112,55 +112,30 @@
 color 200,0,0
 type bed 4
 url http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=
 
 track decipher
 shortLabel DECIPHER CNVs
 longLabel DECIPHER: Chromosomal Imbalance and Phenotype in Humans (CNVs)
 group phenDis
 visibility hide
 color 0,0,0
 type bed 4
 tableBrowser off decipherRaw knownToDecipher knownCanonToDecipher
 prevExonText Left edge
 nextExonText Right edge
 
-track decipherCnv
-shortLabel Decipher CNV New
-longLabel Decipher CNV New
-group phenDis
-visibility hide
-type bigBed 9 +
-itemRgb on
-tableBrowser off
-bigDataUrl /gbdb/$D/decipher/decipherCnv.bb
-url https://decipher.sanger.ac.uk/patient/$$
-urlLabel Decipher Patient View:
-filter.size 0
-filterByRange.size on
-filterLimits.size 2:170487333
-filterValues.variant_class Amplification,Copy-Number Gain,Deletion,Duplication,Duplication/Triplication,Triplication
-filterValues.pathogenicity Benign,Likely Benign,Likely Pathogenic,Pathogenic,Uncertain,Unknown
-mergeSpannedItems on
-searchIndex name
-mouseOverField _mouseOver
-release alpha
-
-searchTable  decipherCnv
-searchMethod exact
-searchType bigBed
-
 track decipherSnvs
 shortLabel DECIPHER SNVs
 longLabel DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs)
 group phenDis
 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
@@ -5480,15 +5455,16 @@
 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 covidGwas.ra alpha