7164821eac1d076015e892bc6b3961f5760f382d
chmalee
  Fri May 8 09:56:05 2020 -0700
Adding NCBI Conflict SVs track as a companion to common svs, refs #25424

diff --git src/hg/makeDb/trackDb/human/trackDb.dbVar.ra src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
index 85b0d4b..6856bac 100644
--- src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
+++ src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
@@ -1,75 +1,110 @@
+track dbVarSv
+superTrack on
+group varRep
+html dbVar_common
+shortLabel NCBI Curated Structural Variants
+longLabel NCBI Curated Structural Variants from dbVar
+
     track dbVar_common
+    superTrack  dbVarSv pack
     group varRep
     compositeTrack on
     visibility pack
     itemRgb on
     type bigBed 9 + .
-shortLabel Common SV
+    shortLabel NCBI Common SV
     longLabel NCBI Curated Common Structural Variants
     mouseOverField label
     searchIndex name
     filterLabel.type Items in Type Field
     filterValues.type alu deletion,copy number gain,copy number loss,copy number variation,deletion,duplication,herv deletion,line1 deletion,sva deletion
     filterLabel.length Items in Length Field
     filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB
     release alpha
 
         track dbVar_common_gnomad
         parent dbVar_common on
         shortLabel NCBI Curated gnomAD SVs
         longLabel NCBI Curated Common SVs: all populations from gnomAD
-    bigDataUrl https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hg19/common_gnomad.bb
+        bigDataUrl /gbdb/$D/bbi/dbVar/common_gnomad.bb
         type bigBed 9 + .
         url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
         urlLabel NCBI Variant Page:
         release alpha
 
         track dbVar_common_1000g
         parent dbVar_common on
         shortLabel NCBI Curated 1000 Genomes SVs
         longLabel NCBI Curated Common SVs: all populations from 1000 Genomes
-    bigDataUrl https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hg19/common_1000g.bb
+        bigDataUrl /gbdb/$D/bbi/dbVar/common_1000g.bb
         type bigBed 9 + .
         url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
         urlLabel NCBI Variant Page:
         release alpha
 
         track dbVar_common_decipher
         parent dbVar_common on
         shortLabel NCBI Curated DECIPHER SVs
         longLabel NCBI Curated Common SVs: all populations from DECIPHER
-    bigDataUrl https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hg19/common_decipher.bb
+        bigDataUrl /gbdb/$D/bbi/dbVar/common_decipher.bb
         type bigBed 9 + .
         url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
         urlLabel NCBI Variant Page:
         release alpha
 
         track dbVar_common_african
         parent dbVar_common on
         shortLabel NCBI Curated African SVs
         longLabel NCBI Curated Common SVs: African
-    bigDataUrl https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hg19/common_african.bb
+        bigDataUrl /gbdb/$D/bbi/dbVar/common_african.bb
         type bigBed 9 + .
         url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
         urlLabel NCBI Variant Page:
         release alpha
 
         track dbVar_common_european
         parent dbVar_common on
         shortLabel NCBI Curated European SVs
         longLabel NCBI Curated Common SVs: European
-    bigDataUrl https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hg19/common_european.bb
+        bigDataUrl /gbdb/$D/bbi/dbVar/common_european.bb
         type bigBed 9 + .
         url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
         urlLabel NCBI Variant Page:
         release alpha
 
         track dbVar_common_global
         parent dbVar_common on
         shortLabel NCBI Curated All Populations
         longLabel NCBI Curated Common SVs: all populations
-    bigDataUrl https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hg19/common_global.bb
+        bigDataUrl /gbdb/$D/bbi/dbVar/common_global.bb
         type bigBed 9 + .
         url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
         urlLabel NCBI Variant Page:
         release alpha
+
+    track dbVar_conflict
+    superTrack dbVarSv pack
+    compositeTrack on
+    visibility pack
+    itemRgb on
+    type bigBed 9 + .
+    shortLabel NCBI Conflict SV
+    longLabel NCBI Curated Conflict Variants
+    mouseOverField label
+    searchIndex name
+    html conflict.html
+    filterLabel.overlap Items in Overlap Field
+    filterValues.overlap 10 to 25,25 to 50,50 to 75,75 to 90,90 to 100
+    filterLabel.type Items in Type Field
+    filterValues.type alu deletion,copy number gain,copy number loss,copy number variation,deletion,duplication,herv deletion,line1 deletion,sva deletion
+    filterLabel.length Items in Length Field
+    filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB
+
+        track dbVar_conflict_pathogenic
+        parent dbVar_conflict on
+        shortLabel NCBI Curated Conflict SVs
+        longLabel NCBI Curated Common SVs: Conflicts with Pathogenic
+        bigDataUrl /gbdb/$D/bbi/dbVar/conflict_pathogenic.bb
+        type bigBed 9 + .
+        url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$
+        urlLabel NCBI Variant Page: