4a1651999514d41b9ed33cbd8ee7ceee08df21eb
Merge parents 9eb4e093778 b937bbf5930
max
  Sat Jun 13 23:28:59 2026 -0700
removing kim

diff --cc src/hg/makeDb/trackDb/human/lrSv.ra
index 0a2042555f0,ec781f1cf8f..6e060aa567d
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@@ -228,51 -228,54 +228,51 @@@
      filter.alleleFreq 0:1
      filterByRange.alleleFreq on
      filterLimits.alleleFreq 0:1
      filterLabel.alleleFreq Allele Frequency
      filter.carrierCount 1:498
      filterByRange.carrierCount on
      filterLabel.carrierCount Number of Carrier Samples
  
      track decodeSv
      parent lrSv
      bigDataUrl /gbdb/$D/lrSv/decodeSv.bb
      shortLabel deCODE 3622 SVs
      longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore)
      type bigBed 9 +
      itemRgb on
-     visibility dense
+     visibility hide
 -    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC (placeholder)
 +    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen
      filterValues.svType DEL,INS,INSDEL
      filterType.svType multipleListOr
      filterLabel.svType SV Type
      filter.svLen 0:861080
      filterByRange.svLen on
      filterLabel.svLen SV Length
      filter.insLen 0:22130
      filterByRange.insLen on
      filterLabel.insLen Insertion Length
 -    filter.AC 0:50
 -    filterByRange.AC on
 -    filterLabel.AC Allele Count (placeholder 50)
      skipEmptyFields on
  
      track hprc2v21Sv
      parent lrSv
      bigDataUrl /gbdb/$D/lrSv/hprc2v21.bb
      shortLabel HPRC v2.1 233 SVs
-     longLabel Structural Variants from the HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus, raw deconstruct)
+     longLabel Structural Variants from HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus)
      type bigBed 9 +
      itemRgb on
-     visibility dense
+     visibility hide
      mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber samples=$nSamples
      filterValues.svType INS,DEL
      filterType.svType multipleListOr
      filterLabel.svType SV Type
      filter.svLen 0:99835
      filterByRange.svLen on
      filterLabel.svLen SV Length
      filter.insLen 0:1064897
      filterByRange.insLen on
      filterLabel.insLen Insertion Length
      filter.AC 0:463
      filterByRange.AC on
      filterLabel.AC Allele Count
      filter.alleleFreq 0:1
      filterByRange.alleleFreq on
@@@ -373,84 -380,86 +377,84 @@@
      filter.AC 1:136
      filterByRange.AC on
      filterLabel.AC Allele Count (carrier haplotypes)
      filter.sampleCount 1:65
      filterByRange.sampleCount on
      filterLabel.sampleCount Sample Count
      filterValues.refTrf True,False
      filterType.refTrf multipleListOr
      filterLabel.refTrf In Tandem Repeat
      filter.refSd 0:1
      filterByRange.refSd on
      filterLimits.refSd 0:1
      filterLabel.refSd Segmental Duplication Overlap
      skipEmptyFields on
  
 -    # kwanhoSv commented out: the Kim PD brain callset is preliminary and
 -    # unpublished (the description page says do not release until publication),
 -    # and carries breakend artifacts up to ~190 Mb. Held off dev/alpha until a
 -    # paper is out. bigBed, .as, converter and makeDoc are retained. The
 -    # pending lrSvAll rebuild will also drop KimPD from databases.tsv so it
 -    # leaves the merged track. refs #36258
 -    #track kwanhoSv
 -    #parent lrSv
 -    #bigDataUrl /gbdb/$D/lrSv/kwanho.bb
 -    #shortLabel Kim PD 100 prelim
 -    #longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) - PRELIMINARY, data to be updated, contact the authors before using
 -    #type bigBed 9 +
 -    #itemRgb on
 -    #visibility dense
 -    #mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC AF_PD=$afPd AF_HC=$afHc diff=$differentialRate
 -    #filterValues.svType DEL,INS,DUP,INV
 -    #filterType.svType multipleListOr
 -    #filterLabel.svType SV Type
 -    #filter.svLen 0:200000000
 -    #filterByRange.svLen on
 -    #filterLabel.svLen SV Length
 -    #filter.insLen 0:20145
 -    #filterByRange.insLen on
 -    #filterLabel.insLen Insertion Length
 -    #filter.AC 0:200
 -    #filterByRange.AC on
 -    #filterLabel.AC Allele Count (PD+HC+ILBD)
 -    #filter.qual 0:100
 -    #filterByRange.qual on
 -    #filterLabel.qual Quality
 -    #filter.afPd 0:1
 -    #filterByRange.afPd on
 -    #filterLimits.afPd 0:1
 -    #filterLabel.afPd Allele Frequency (PD)
 -    #filter.afHc 0:1
 -    #filterByRange.afHc on
 -    #filterLimits.afHc 0:1
 -    #filterLabel.afHc Allele Frequency (HC)
 -    #filter.afIlbd 0:1
 -    #filterByRange.afIlbd on
 -    #filterLimits.afIlbd 0:1
 -    #filterLabel.afIlbd Allele Frequency (ILBD)
 -    #filter.differentialRate -1:1
 -    #filterByRange.differentialRate on
 -    #filterLimits.differentialRate -1:1
 -    #filterLabel.differentialRate Case-Control Differential (case - control)
 -    #skipEmptyFields on
 +    # NOT FOR RELEASE: preliminary and unpublished (Kim et al. 2026 not out yet),
 +    # and the callset has breakend artifacts up to 190 Mb (e.g. a single "INV"
 +    # spanning all of chr4). Held on dev/alpha and kept out of the lrSvAll merge
 +    # (removed from databases.tsv) until the data is published and cleaned.
 +    track kwanhoSv
 +    parent lrSv
 +    bigDataUrl /gbdb/$D/lrSv/kwanho.bb
 +    shortLabel Kim PD 100 prelim
 +    longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) - PRELIMINARY, data to be updated, contact the authors before using
 +    type bigBed 9 +
 +    itemRgb on
 +    visibility dense
 +    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC AF_PD=$afPd AF_HC=$afHc diff=$differentialRate
 +    filterValues.svType DEL,INS,DUP,INV
 +    filterType.svType multipleListOr
 +    filterLabel.svType SV Type
 +    filter.svLen 0:200000000
 +    filterByRange.svLen on
 +    filterLabel.svLen SV Length
 +    filter.insLen 0:20145
 +    filterByRange.insLen on
 +    filterLabel.insLen Insertion Length
 +    filter.AC 0:200
 +    filterByRange.AC on
 +    filterLabel.AC Allele Count (PD+HC+ILBD)
 +    filter.qual 0:100
 +    filterByRange.qual on
 +    filterLabel.qual Quality
 +    filter.afPd 0:1
 +    filterByRange.afPd on
 +    filterLimits.afPd 0:1
 +    filterLabel.afPd Allele Frequency (PD)
 +    filter.afHc 0:1
 +    filterByRange.afHc on
 +    filterLimits.afHc 0:1
 +    filterLabel.afHc Allele Frequency (HC)
 +    filter.afIlbd 0:1
 +    filterByRange.afIlbd on
 +    filterLimits.afIlbd 0:1
 +    filterLabel.afIlbd Allele Frequency (ILBD)
 +    filter.differentialRate -1:1
 +    filterByRange.differentialRate on
 +    filterLimits.differentialRate -1:1
 +    filterLabel.differentialRate Case-Control Differential (case - control)
 +    skipEmptyFields on
  
      track aprSv
      parent lrSv
      bigDataUrl /gbdb/$D/lrSv/apr.bb
      shortLabel Arab APR 53 SVs
      longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples)
      type bigBed 9 +
      itemRgb on
-     visibility dense
+     visibility hide
      mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts
      filterValues.svType INS,DEL,CPX,MIXED
      filterType.svType multipleListOr
      filterLabel.svType SV Type
      filter.svLen 0:99885
      filterByRange.svLen on
      filterLabel.svLen SV Length
      filter.insLen 0:584016
      filterByRange.insLen on
      filterLabel.insLen Insertion Length
      filter.AC 0:107
      filterByRange.AC on
      filterLabel.AC Allele Count
      filterByRange.alleleFreq on
      filterLimits.alleleFreq 0:1