f058c8fe4601b223ff47468eb3525c05ccd03850
max
  Wed Apr 22 09:17:17 2026 -0700
srSv: new short-read SV supertrack, split out of lrSv

Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr,
tommoJpCnv) out of the Long-read SV supertrack into a new sibling
supertrack srSv (Short-read SVs), so the lrSv collection contains
only long-read callsets. Filter fields (svType, svLen, insLen, AC)
are mirrored at the srSv supertrack level to keep the UX parallel
to lrSv.

- trackDb: new human/srSv.ra with the three subtrack stanzas and
updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas
removed from human/lrSv.ra. human/trackDb.ra now includes
srSv.ra. Also a new human/srSv.html overview page; the SR rows
and SR-specific paragraphs removed from human/lrSv.html.
- Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/
{lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to
scripts/srSv/ with git mv (history preserved) and renamed to
drop the "lrSv" prefix. Internal path references in abelSvBuild.sh
and abelSvVcfToBed.py updated.
- makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and
extended with the onekg3202Sr and tommoJpCnv sections moved from
lrSv.txt. lrSv.txt leaves a pointer.
- Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr,
lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*.
/gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and
/gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/.

refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 2f553ecbf1e..777dc5bd0bd 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -1,584 +1,470 @@
 track lrSv
 superTrack on
 shortLabel Long-read SVs
 longLabel Structural Variants from Long-read Sequencing
 group varRep
 visibility hide
 # Supertrack-level filters. These are rendered on the supertrack's own
 # hgTrackUi page (superTrackUi in hgTrackUi.c). Cart values stored under
 # "lrSv.filter.<field>.min/max" are inherited at read time by every
 # subtrack via cartOptionalStringClosestToHome() walking tdb->parent. A
 # subtrack-level filter always wins over the supertrack-level one.
 filterValues.svType DEL,INS,INV,CPX,DUP,CNV,CTX,INSDEL,MIXED,BND,MEI,TRA
 filterType.svType multipleListOr
 filterLabel.svType SV Type
 filter.svLen 0:250000000
 filterByRange.svLen on
 filterLabel.svLen SV Length (bp)
 filter.insLen 0:30176500
 filterByRange.insLen on
 filterLabel.insLen Insertion Length (bp)
 filter.AC 0:30000
 filterByRange.AC on
 filterLabel.AC Allele Count
 noScoreFilter on
 
     track colorsDbSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb
     shortLabel CoLoRSdb 1427 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) svLen=$svLen insLen=$insLen AF=$AF AC=$AC/$AN (Hom:$acHom Het:$acHet Hemi:$acHemi) samples=$NS
     searchIndex name
     filterValues.svType DEL,INS,INV,DUP
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:101381
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:18724
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.AC 0:2854
     filterByRange.AC on
     filterLabel.AC Alt Allele Count (AC)
     filter.AF 0:1
     filterByRange.AF on
     filterLimits.AF 0:1
     filterLabel.AF Allele Frequency (AF)
     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> ($svType) svLen=$svLen insLen=$insLen type=$insType family=$family AC=$AC AF=$alleleFreq
     filterValues.svType DEL,INS,CPX
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     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
     filter.svLen 0:49171
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:48091
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.AC 0:1816
     filterByRange.AC on
     filterLabel.AC Allele Count
     skipEmptyFields on
     dataVersion 1.1
     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> ($svType) svLen=$svLen insLen=$insLen AF=$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.svLen on
-    filter.svLen 0:250000000
-    filterLimits.svLen -1:250000000
-    filterLabel.svLen SV Length (bp; -1 for BND)
-    filter.insLen 0:8545
-    filterByRange.insLen on
-    filterLabel.insLen Insertion Length
-    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> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber popMax=$popmaxAf
-    filterValues.svType DEL,INS,DUP,INV,CPX,CTX,CNV
-    filterType.svType multipleListOr
-    filterLabel.svType SV Type
-    filter.svLen 0:154807729
-    filterByRange.svLen on
-    filterLabel.svLen SV Length
-    filter.insLen 0:178243
-    filterByRange.insLen on
-    filterLabel.insLen Insertion Length
-    filter.AC 0:6404
-    filterByRange.AC on
-    filterLabel.AC Allele Count
-    filter.alleleFreq 0:1
-    filterByRange.alleleFreq on
-    filterLimits.alleleFreq 0:1
-    filterLabel.alleleFreq Allele Frequency (all)
-    filter.popmaxAf 0:1
-    filterByRange.popmaxAf on
-    filterLimits.popmaxAf 0:1
-    filterLabel.popmaxAf Population Max AF
-    filter.afAfr 0:1
-    filterByRange.afAfr on
-    filterLimits.afAfr 0:1
-    filterLabel.afAfr AF African
-    filter.afEur 0:1
-    filterByRange.afEur on
-    filterLimits.afEur 0:1
-    filterLabel.afEur AF European
-    skipEmptyFields on
-
     track gustafsonSv
     parent lrSv
     bigDataUrl /gbdb/$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) svLen=$svLen insLen=$insLen AC=$AC samples=$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.insLen 0:25094
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:200
     filterByRange.AC on
     filterLabel.AC Allele Count (placeholder)
     filter.sampleCount 1:100
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Carrier Samples
     skipEmptyFields on
     priority 3
 
     track aou1kSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/aou1k.bb
     shortLabel AoU 1027 SVs
     longLabel Structural Variants from 1,027 AoU Individuals (PacBio HiFi Long-read)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC~$AC AF_AFR=$afAfr AF_EUR=$afEur
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:9905
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:9998
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:2054
     filterByRange.AC on
     filterLabel.AC Allele Count (approx)
     filterByRange.afAfr on
     filterLimits.afAfr 0:1
     filterLabel.afAfr AF African
     filterByRange.afEur on
     filterLimits.afEur 0:1
     filterLabel.afEur AF European
     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> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC samples=$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.insLen 0:27242
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:1890
     filterByRange.AC on
     filterLabel.AC Allele Count (approx 2*SUPP)
     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/$D/lrSv/tommoJp.bb
     shortLabel ToMMo 333 SVs
     longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99985
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:30649
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.AC 0:444
     filterByRange.AC on
     filterLabel.AC Allele Count
 
     track ga4kSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb
     shortLabel GA4K 502 SVs
     longLabel Structural Variants from 502 Children's Mercy GA4K Probands and Families (PacBio HiFi)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC~$AC 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.insLen 0:14923
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:996
     filterByRange.AC on
     filterLabel.AC Allele Count (approx)
     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/$D/lrSv/decodeSv.bb
     shortLabel deCODE 3622 SVs
     longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC (placeholder)
     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 hprc2Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hprc2.bb
     shortLabel HPRC v2 233 SVs
     longLabel Structural Variants from the HPRC v2 Pangenome Graph (233 Samples, minigraph-cactus + vcfwave)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber samples=$nSamples
     filterValues.svType INS,DEL,CPX,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99113
     filterByRange.svLen on
     filterLabel.svLen SV Length
     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 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
     filter.insLen 0:108546
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 1:35
     filterByRange.AC on
     filterLabel.AC 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> ($svType) svLen=$svLen insLen=$insLen samples=$sampleCount AC=$AC
     filterValues.svType DEL,INS,INV
     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 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
 
     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/$D/lrSv/apr.bb
     shortLabel Arab APR 53 SVs
     longLabel Structural Variants from Arabic Pangenome Reference (53 UAE-resident Arab samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$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
     filterLabel.alleleFreq Allele Frequency
     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> ($svType) svLen=$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 0:8998096
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:376583
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:116
     filterByRange.AC on
     filterLabel.AC Allele Count
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     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> ($svType) svLen=$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