5e4ca58df1b5bfe554fe5cc3309a39736ca256ee
max
Tue Apr 21 08:08:52 2026 -0700
cpc1Sv: restrict to the 58 CPC samples, drop HPRC-specific SVs
Rewrite lrSvCpc1VcfToBed.py to identify the 58 CPC sample columns by
name prefix (HIFI032* or RY*), recompute AC/AN/NS from those GT
columns only, and skip any snarl that no CPC sample carries. The
HPRC portion is already represented elsewhere in lrSv, so this keeps
the track population-consistent with its label.
Rebuild results: 46,092 snarl sites on hs1 (down from 97,205 when
combined with HPRC), 36,030 lifted to hg38 (down from 81,261;
10,062 unmapped). Updates cpc1Sv.html, lrSv.ra labels, and the
makeDoc.
refs #36258
diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 39431a27917..2fb6a445a4e 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -1,449 +1,450 @@
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 $name ($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 $name ($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 $name ($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 $name ($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 $name ($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 $name ($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 $name ($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 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 $name ($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 $name ($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 $name ($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 $name ($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 $name ($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 $name ($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 $name ($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 $name ($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+HPRC 105 SVs
- longLabel Structural Variants from CPC + HPRC Phase 1 Pangenome (105 samples, 58 Chinese + 47 HPRC)
+ 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 $name ($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 $name ($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