3bf9e1a841206d3bf5902e06791ef5be2dbdbd39
max
  Fri Jul 17 09:09:47 2026 -0700
lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv)

#Preview2 week - bugs introduced now will need a build patch to fix
888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with
per-superpopulation allele frequencies, imputation-accuracy metrics and UK
Biobank SV-WAS associations. Converter approximates AC/AN from AF and the
genotype missing rate (source has no allele count), stores BND mate breakends,
and follows the shared lrSv svType/svLen/insLen/AC field convention so the
container-level filters apply. refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index bfb4f3ba0be..ee7ba629c4a 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -533,30 +533,84 @@
     filterLabel.insLen Insertion Length
     filter.AC 1:351
     filterByRange.AC on
     filterLabel.AC Carrier Count
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.nabecCount 0:205
     filterByRange.nabecCount on
     filterLabel.nabecCount NABEC Carriers (European ancestry)
     filter.hbccCount 0:146
     filterByRange.hbccCount on
     filterLabel.hbccCount HBCC Carriers (African/African-admixed ancestry)
 
+    track noyvertSv
+    parent longReadVariants
+    bigDataUrl /gbdb/$D/lrSv/noyvert.bb
+    shortLabel Noyvert 888 SVs
+    longLabel Structural Variants from 888 Multi-ancestry Individuals (Oxford Nanopore, Noyvert et al. 2025)
+    type bigBed 9 +
+    itemRgb on
+    visibility hide
+    mouseOver <b>Var</b>: ${name} (${svType})<br><b>SV len</b>: ${svLen}<br><b>Ins len</b>: ${insLen}<br><b>AF</b>: ${AF}<br><b>AC</b>: ${AC}/${AN}<br><b>GWAS hits</b>: ${nGwas}
+    filterValues.svType DEL,INS,INV,DUP,BND
+    filterType.svType multipleListOr
+    filterLabel.svType SV Type
+    filter.svLen 0:28634664
+    filterByRange.svLen on
+    filterLabel.svLen SV Length (bp)
+    filter.insLen 0:45109
+    filterByRange.insLen on
+    filterLabel.insLen Insertion Length (bp)
+    filter.AC 0:1776
+    filterByRange.AC on
+    filterLabel.AC Allele Count (approx)
+    filter.AF 0:1
+    filterByRange.AF on
+    filterLimits.AF 0:1
+    filterLabel.AF Allele Frequency
+    filter.afAfr 0:1
+    filterByRange.afAfr on
+    filterLimits.afAfr 0:1
+    filterLabel.afAfr AF African
+    filter.afAmr 0:1
+    filterByRange.afAmr on
+    filterLimits.afAmr 0:1
+    filterLabel.afAmr AF Admixed American
+    filter.afEas 0:1
+    filterByRange.afEas on
+    filterLimits.afEas 0:1
+    filterLabel.afEas AF East Asian
+    filter.afEur 0:1
+    filterByRange.afEur on
+    filterLimits.afEur 0:1
+    filterLabel.afEur AF European
+    filter.afSas 0:1
+    filterByRange.afSas on
+    filterLimits.afSas 0:1
+    filterLabel.afSas AF South Asian
+    filter.nGwas 0:11
+    filterByRange.nGwas on
+    filterLabel.nGwas UK Biobank GWAS Hit Count
+    filter.r2Ukb 0:1
+    filterByRange.r2Ukb on
+    filterLimits.r2Ukb 0:1
+    filterLabel.r2Ukb Imputation r2 (UK Biobank)
+    skipEmptyFields on
+
     # NOT FOR RELEASE: data received from Eichler lab via email, not yet published.
     # Do not add to lrSvAll merged track until a preprint or paper is available.
     track lrSv1kLin
     parent longReadVariants
     release alpha
     bigDataUrl /gbdb/$D/lrSv/lin1218.bb
     shortLabel 1KG Linear 1218 SVs
     longLabel Structural Variants from 1,218 Individuals (1000 Genomes, Linear Long-read)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$AN<br><b>AF</b>: $AF<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur<br><b>Samples</b>: $NS
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type