06a482a2120d4d85c7c34fb5038213e07f595554
max
  Tue Apr 21 15:00:21 2026 -0700
lrSv: add tommoJpCnv short-read CNV comparator (multiWig)

ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies
from short-read whole-genome sequencing of 48,874 Japanese individuals
(jMorp 20230828 release, GATK CNV germline workflow at 1 kb
resolution). Published as a companion short-read comparator to the
long-read tommoJpSv track.

Rendered as a multiWig container with two bigWig subtracks (transparent
overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and
tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are
absolute carrier counts out of 48,874. 2,006,905 bins with at least one
CNV carrier; bins that are wholly CN=2 are omitted.

Files:
- trackDb/human/lrSv.ra: new tommoJpCnv multiWig container
- trackDb/human/tommoJpCnv.html: new doc page
- trackDb/human/lrSv.html: summary-table row + per-track blurb
- scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs
- doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps

refs #36258

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 2fb6a445a4e..ca027b343a1 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -1,450 +1,483 @@
 track lrSv
 superTrack on
 shortLabel Long-read SVs
 longLabel Structural Variants from Long-read Sequencing
 group varRep
 visibility hide
 
     track colorsDbSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb
     shortLabel CoLoRSdb 1,427 SVs
     longLabel Structural Variants from CoLoRSdb (Consortium of Long-Read Sequencing, 1,427 Samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     dataVersion v1.2.0
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$af AC=$AC (Hom:$AC_Hom Het:$AC_Het Hemi:$AC_Hemi) samples=$NS
     searchIndex name
     filterValues.svType DEL,INS,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 20:101381
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.AC 0:2854
     filterByRange.AC on
     filterLabel.AC Alt Allele Count (AC)
     skipEmptyFields on
     priority 1
 
     track lrSv1kgOnt
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/1kgOnt.bb
     shortLabel 1KG ONT 1019 SVs
     longLabel Structural Variants from 1,019 Diverse Humans (Vienna ONT, Schloissnig et al. 2025)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svClass) len=$svLen type=$insType family=$family AC=$alleleCount AF=$alleleFreq
     filterValues.svClass DEL,INS,COMPLEX
     filterType.svClass multipleListOr
     filterLabel.svClass SV Class
     filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo
     filterType.insType multipleListOr
     filterLabel.insType Insertion/Deletion Type
     filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA
     filterType.family multipleListOr
     filterLabel.family Transposon Family
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count
     skipEmptyFields on
     priority 2
 
     track abelSv
     parent lrSv
     bigDataUrl /gbdb/$D/abelSv/abelSv.bb
     shortLabel CCDG 17795 SR SVs
     longLabel Structural Variants from 17,795 Genomes - Illumina SHORT-READ CCDG callset (Abel et al. 2020) - included for comparison
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLength AF=$af AC=$ac/$an callset=$callset MSQ=$msq
     skipEmptyFields on
     skipFields mateChrom,matePos
     filterValues.svType DEL|deletion,DUP|duplication,INV|inversion,MEI|mobile element insertion,BND|breakend/translocation
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filterValues.callset B38|Native GRCh38 callset (14623 samples),B37lift|Lifted from GRCh37 callset (8417 samples)
     filterType.callset multipleListOr
     filterLabel.callset Source Callset
     filterValues.filter PASS|High confidence,LOW|Low confidence
     filterType.filter multipleListOr
     filterLabel.filter Filter Status
     filterByRange.af on
     filter.af 0:1
     filterLimits.af 0:1
     filterLabel.af Allele Frequency (AF)
     filterByRange.svLength on
     filter.svLength 0:250000000
     filterLimits.svLength -1:250000000
     filterLabel.svLength SV Length (bp; -1 for BND)
     filterByRange.msq on
     filter.msq 0:500
     filterLimits.msq 0:500
     filterLabel.msq Mean Sample Quality (MSQ)
     filterByRange.ac on
     filter.ac 0:30000
     filterLimits.ac 0:30000
     filterLabel.ac Allele Count (AC)
     url https://www.nature.com/articles/s41586-020-2371-0
     urlLabel Abel et al, Nature 2020:
 
     track onekg3202Sr
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/onekg3202sr.bb
     shortLabel 1KG 3202 SR SVs
     longLabel 1000 Genomes 3202-sample Illumina SHORT-READ GATK-SV callset (Byrska-Bishop 2022) - included for comparison
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$alleleFreq AC=$alleleCount/$alleleNumber popMax=$popmaxAf
     filterValues.svType DEL,INS,DUP,INV,CPX,CTX,CNV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:154807729
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency (all)
     filter.popmaxAf 0:1
     filterByRange.popmaxAf on
     filterLimits.popmaxAf 0:1
     filterLabel.popmaxAf Population Max AF
     filter.afAfr 0:1
     filterByRange.afAfr on
     filterLimits.afAfr 0:1
     filterLabel.afAfr AF African
     filter.afEur 0:1
     filterByRange.afEur on
     filterLimits.afEur 0:1
     filterLabel.afEur AF European
     skipEmptyFields on
 
     track gustafsonSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/gustafson.bb
     shortLabel 1KG ONT 100 SVs
     longLabel Structural Variants from 100 1000 Genomes ONT Samples (Gustafson et al. 2024)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen samples=$sampleCount
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:98289
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.sampleCount 1:100
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Carrier Samples
     skipEmptyFields on
     priority 3
 
     track aou1kSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/aou1k.bb
     shortLabel AoU 1K SVs
     longLabel Structural Variants from 1,027 AoU Individuals (PacBio HiFi Long-read)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AF_AFR=$afAfr AF_EUR=$afEur
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     #filter.svLen 50:9998
     filterByRange.svLen on
     filterLabel.svLen SV Length
     #filter.afAfr 0:1
     filterByRange.afAfr on
     filterLimits.afAfr 0:1
     filterLabel.afAfr AF African
     #filter.afEur 0:1
     filterByRange.afEur on
     filterLimits.afEur 0:1
     filterLabel.afEur AF European
     #filter.afEas 0:1
     filterByRange.afEas on
     filterLimits.afEas 0:1
     filterLabel.afEas AF East Asian
     skipEmptyFields on
 
     track han945Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/han945.bb
     shortLabel Han 945 SVs
     longLabel Structural Variants from 945 Han Chinese (Long-read Sequencing)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$alleleFreq samples=$sampleCount
     filterValues.svType DEL,INS,DUP,INV,TRA
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99743
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.sampleCount 1:945
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Supporting Samples
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     skipEmptyFields on
     urls chr2="hgTracks?position=$$"
 
+    track tommoJpCnv
+    parent lrSv
+    container multiWig
+    aggregate transparentOverlay
+    showSubtrackColorOnUi on
+    shortLabel ToMMo 48K CNV SR
+    longLabel CNV Carrier Counts from 48,874 Japanese Individuals (ToMMo 48KJPN-CNV, short-read WGS; 1 kb bins) - included for comparison
+    type bigWig 0 48874
+    autoScale on
+    viewLimits 0:1000
+    viewLimitsMax 0:48874
+    maxHeightPixels 100:32:8
+    visibility full
+    priority 2.5
+
+        track tommoJpCnvLoss
+        parent tommoJpCnv
+        bigDataUrl /gbdb/$D/lrSv/tommoJpCnvLoss.bw
+        shortLabel ToMMo CNV Loss
+        longLabel Samples with copy-number loss (CN<2) per 1 kb bin, ToMMo 48KJPN-CNV
+        type bigWig 0 48874
+        color 200,0,0
+        altColor 200,0,0
+
+        track tommoJpCnvGain
+        parent tommoJpCnv
+        bigDataUrl /gbdb/$D/lrSv/tommoJpCnvGain.bw
+        shortLabel ToMMo CNV Gain
+        longLabel Samples with copy-number gain (CN>2) per 1 kb bin, ToMMo 48KJPN-CNV
+        type bigWig 0 48874
+        color 0,160,0
+        altColor 0,160,0
+
     track tommoJpSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/tommoJp.bb
     shortLabel ToMMo Japanese SVs
     longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$alleleFreq AC=$alleleCount
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 51:99980
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.alleleCount 0:444
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count
 
     track ga4kSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb
     shortLabel GA4K SVs
     longLabel Structural Variants from 502 Children's Mercy GA4K Probands and Families (PacBio HiFi)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$alleleFreq carriers=$carrierCount/$sampleTotal
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:809711
     filterByRange.svLen on
     filterLabel.svLen SV Length
     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/$D/lrSv/decodeSv.bb
     shortLabel deCODE 3,622 SVs
     longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen
     filterValues.svType DEL,INS,INSDEL
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:861080
     filterByRange.svLen on
     filterLabel.svLen SV Length
     skipEmptyFields on
 
     track hprc2Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hprc2.bb
     shortLabel HPRC v2 SVs
     longLabel Structural Variants from the HPRC v2 Pangenome Graph (233 Samples, minigraph-cactus + vcfwave)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$alleleFreq AC=$alleleCount/$alleleNumber samples=$nSamples
     filterValues.svType INS,DEL,COMPLEX,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 50:97718
     filterByRange.svLen on
     filterLabel.svLen SV Length
     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 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> ($svType) len=$svLen samples=$sampleCount alleles=$alleleCount 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
     filter.alleleCount 1:35
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count (carrier haplotypes)
     filter.sampleCount 1:35
     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
 
     track hgsvc3Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hgsvc3.bb
     shortLabel HGSVC3 65 SVs
     longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen samples=$sampleCount alleles=$alleleCount
     filterValues.svType DEL,INS,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:30176500
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.alleleCount 1:136
     filterByRange.alleleCount on
     filterLabel.alleleCount 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
 
     track kwanhoSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/kwanho.bb
     shortLabel Kim PD Brain SVs (preliminary)
     longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) - PRELIMINARY, data to be updated, contact the authors before using
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen 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.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/$D/lrSv/apr.bb
     shortLabel Arab APR 53 SVs
     longLabel Structural Variants from Arabic Pangenome Reference (53 UAE-resident Arab samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AC=$alleleCount/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count
     skipEmptyFields on
 
     track cpc1Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/cpc1.bb
     shortLabel CPC 58 SVs
     longLabel Structural Variants from Chinese Pangenome Consortium (58 samples, CPC portion of the CPC+HPRC graph; HPRC-specific SVs removed)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AC=$alleleCount/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count
     skipEmptyFields on
 
     track chirmade101Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/chirmade101.bb
     shortLabel SVatalog 101 SVs
     longLabel Structural Variants from 101 Long-read Whole-Genome Sequences (GWAS SVatalog, Chirmade et al. 2026)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen genes=$geneCount
     filterValues.svType del,ins,dup,inv,complex
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:1321484
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.geneCount 0:200
     filterByRange.geneCount on
     filterLabel.geneCount Gene Count
     skipEmptyFields on