038bd0cd3f7c84ee984905608dfdd27d02cc61ec
max
  Tue Jun 2 05:19:51 2026 -0700
[Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1)

Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged
with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS,
AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published.
hg38: 587,779 SVs; hs1: 614,522 SVs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

, refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 9244f30c19c..04e990000cd 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -275,30 +275,66 @@
     filter.insLen 0:97718
     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
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.snarlLevel 0:10
     filterByRange.snarlLevel on
     filterLabel.snarlLevel Snarl Level
     skipEmptyFields on
 
+    track hprc2JasmineSv
+    parent lrSv
+    bigDataUrl /gbdb/$D/lrSv/hprc2Jasmine.bb
+    shortLabel HPRC2 Jasmine 231 SVs
+    longLabel Structural Variants from 231 HPRC v2 Assemblies (14 SV Callers, Jasmine-merged; Hall Lab / Liao)
+    type bigBed 9 +
+    itemRgb on
+    visibility dense
+    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$nSamples/$alleleNumber AF=$alleleFreq callers=$nCallers ($callers)
+    filterValues.svType DEL,INS
+    filterType.svType multipleListOr
+    filterLabel.svType SV Type
+    filter.svLen 0:30176500
+    filterByRange.svLen on
+    filterLabel.svLen SV Length
+    filter.insLen 0:30176500
+    filterByRange.insLen on
+    filterLabel.insLen Insertion Length
+    filter.AC 0:231
+    filterByRange.AC on
+    filterLabel.AC Carrier Sample Count
+    filter.alleleFreq 0:1
+    filterByRange.alleleFreq on
+    filterLimits.alleleFreq 0:1
+    filterLabel.alleleFreq Carrier Frequency
+    filter.nCallers 1:14
+    filterByRange.nCallers on
+    filterLabel.nCallers Number of Supporting Callers
+    filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish
+    filterType.callers multipleListAnd
+    filterLabel.callers Supporting Callers
+    filterValues.sources PAV,dipcall,longcallD
+    filterType.sources multipleListAnd
+    filterLabel.sources Source Pipeline
+    skipEmptyFields on
+
     track hgsvc2Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb
     shortLabel HGSVC2 32 SVs
     longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert et al. 2021)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$sampleCount AC=$AC AF=$popAllAf
     filterValues.svType DEL,INS,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:57207414
     filterByRange.svLen on
     filterLabel.svLen SV Length
@@ -458,15 +494,63 @@
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen genes=$geneCount
     filterValues.svType DEL,INS,DUP,INV,CPX
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:1321484
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:31711
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.geneCount 0:200
     filterByRange.geneCount on
     filterLabel.geneCount Gene Count
     skipEmptyFields on
 
+    # NOT FOR RELEASE: data received from Eichler lab via email, not yet published.
+    # Do not add to lrSvAll merged track until a preprint or paper is available.
+    track lrSv1kLin
+    parent lrSv
+    bigDataUrl /gbdb/$D/lrSv/lin1218.bb
+    shortLabel 1KG Linear 1218 SVs
+    longLabel Structural Variants from 1,218 Individuals (1000 Genomes, Linear Long-read Sequencing)
+    type bigBed 9 +
+    itemRgb on
+    visibility dense
+    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$AN AF=$AF AF_AFR=$afAfr AF_EUR=$afEur samples=$NS
+    searchIndex name
+    filterValues.svType DEL,INS
+    filterType.svType multipleListOr
+    filterLabel.svType SV Type
+    filter.svLen 0:99565
+    filterByRange.svLen on
+    filterLabel.svLen SV Length (bp)
+    filter.insLen 0:99968
+    filterByRange.insLen on
+    filterLabel.insLen Insertion Length (bp)
+    filter.AC 0:2436
+    filterByRange.AC on
+    filterLabel.AC Allele Count
+    filter.AF 0:1
+    filterByRange.AF on
+    filterLimits.AF 0:1
+    filterLabel.AF Allele Frequency
+    filterByRange.afAfr on
+    filterLimits.afAfr 0:1
+    filterLabel.afAfr AF African
+    filterByRange.afAmr on
+    filterLimits.afAmr 0:1
+    filterLabel.afAmr AF Admixed American
+    filterByRange.afEas on
+    filterLimits.afEas 0:1
+    filterLabel.afEas AF East Asian
+    filterByRange.afEur on
+    filterLimits.afEur 0:1
+    filterLabel.afEur AF European
+    filterByRange.afSas on
+    filterLimits.afSas 0:1
+    filterLabel.afSas AF South Asian
+    filter.NS 1:1218
+    filterByRange.NS on
+    filterLabel.NS Samples with Genotype Data
+    skipEmptyFields on
+