1b074613b1c6b7f84953c3f490631b91d844c9a9
galt
  Thu Sep 8 22:40:20 2022 -0700
Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 7645fc5..a593f8a 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -1699,55 +1699,59 @@
         1624|3_prime_UTR_variant,\
         1619|nc_transcript_variant,\
         2153|genic_upstream_transcript_variant,\
         1986|upstream_transcript_variant,\
         2152|genic_downstream_transcript_variant,\
         1987|downstream_transcript_variant,\
         1627|intron_variant
     maxFuncImpactFilterType multipleListOr
 
         track dbSnp153Common
         parent dbSnp153ViewVariants on
         subGroups view=variants
         shortLabel Common dbSNP(153)
         longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153
         bigDataUrl /gbdb/$D/snp/dbSnp153Common.bb
+        defaultGeneTracks knownGene
         priority 1
 
         track dbSnp153ClinVar
         parent dbSnp153ViewVariants off
         subGroups view=variants
         shortLabel dbSNP(153) in ClinVar
         longLabel Short Genetic Variants from dbSNP Release 153 Included in ClinVar
         bigDataUrl /gbdb/$D/snp/dbSnp153ClinVar.bb
+        defaultGeneTracks knownGene
         priority 2
 
         track dbSnp153Mult
         parent dbSnp153ViewVariants off
         subGroups view=variants
         shortLabel dbSNP(153) Mult.
         longLabel Short Genetic Variants from dbSNP Release 153 that Map to Multiple Genomic Loci
         bigDataUrl /gbdb/$D/snp/dbSnp153Mult.bb
+        defaultGeneTracks knownGene
         priority 3
 
         track dbSnp153
         parent dbSnp153ViewVariants off
         subGroups view=variants
         shortLabel All dbSNP(153)
         longLabel All Short Genetic Variants from dbSNP Release 153
         bigDataUrl /gbdb/$D/snp/dbSnp153.bb
         maxWindowToDraw 1000000
+        defaultGeneTracks knownGene
         priority 4
 
     track dbSnp153ViewErrs
     parent dbSnp153Composite
     view errs
     shortLabel Mapping Errors
     visibility dense
 
         track dbSnp153BadCoords
         parent dbSnp153ViewErrs off
         subGroups view=errs
         shortLabel Map Err dbSnp(153)
         longLabel Mappings with Inconsistent Coordinates from dbSNP 153
         bigDataUrl /gbdb/$D/snp/dbSnp153BadCoords.bb
         type bigBed 4
@@ -1821,54 +1825,58 @@
         1623|5_prime_UTR_variant,\
         1624|3_prime_UTR_variant,\
         1619|nc_transcript_variant,\
         2|genic_upstream_transcript_variant,\
         1986|upstream_transcript_variant,\
         2152|genic_downstream_transcript_variant,\
         1987|downstream_transcript_variant,\
         1627|intron_variant
     maxFuncImpactFilterType multipleListOr
 
         track dbSnp155Common
         parent dbSnp155ViewVariants on
         subGroups view=variants
         shortLabel Common dbSNP(155)
         longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 155
+        defaultGeneTracks knownGene
         bigDataUrl /gbdb/$D/snp/dbSnp155Common.bb
         priority 1
 
         track dbSnp155ClinVar
         parent dbSnp155ViewVariants off
         subGroups view=variants
         shortLabel ClinVar dbSNP(155)
         longLabel Short Genetic Variants from dbSNP Release 155 Included in ClinVar
+        defaultGeneTracks knownGene
         bigDataUrl /gbdb/$D/snp/dbSnp155ClinVar.bb
         priority 2
 
         track dbSnp155Mult
         parent dbSnp155ViewVariants off
         subGroups view=variants
         shortLabel Mult. dbSNP(155)
         longLabel Short Genetic Variants from dbSNP Release 155 that Map to Multiple Genomic Loci
+        defaultGeneTracks knownGene
         bigDataUrl /gbdb/$D/snp/dbSnp155Mult.bb
         priority 3
 
         track dbSnp155
         parent dbSnp155ViewVariants off
         subGroups view=variants
         shortLabel All dbSNP(155)
         longLabel All Short Genetic Variants from dbSNP Release 155
+        defaultGeneTracks knownGene
         bigDataUrl /gbdb/$D/snp/dbSnp155.bb
         maxWindowToDraw 1000000
         priority 4
 
     track dbSnp155ViewErrs
     parent dbSnp155Composite
     view errs
     shortLabel Mapping Errors
     visibility dense
 
         track dbSnp155BadCoords
         parent dbSnp155ViewErrs off
         subGroups view=errs
         shortLabel Map Err dbSnp(155)
         longLabel Mappings with Inconsistent Coordinates from dbSNP 155