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 @@ -1,472 +1,556 @@ 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|DEL (Deletion),INS|INS (Insertion),INV|INV (Inversion),CPX|CPX (Complex rearrangement),DUP|DUP (Duplication),CNV|CNV (Copy-number variant),CTX|CTX (Chromosomal translocation),INSDEL|INSDEL (Insertion-deletion),MIXED|MIXED (multi-allele snarl),BND|BND (Breakend / translocation),MEI|MEI (Mobile element insertion),TRA|TRA (Translocation) 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 include lrSvAll.ra 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 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 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=$nSamples filterValues.svType INS,DEL,CPX,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99113 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:97718 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:463 filterByRange.AC on filterLabel.AC Allele Count filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.snarlLevel 0:10 filterByRange.snarlLevel on filterLabel.snarlLevel Snarl Level skipEmptyFields on + track hprc2JasmineSv + parent lrSv + bigDataUrl /gbdb/$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=$popAllAf filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:57207414 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:108546 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 1:35 filterByRange.AC on filterLabel.AC Allele Count (carrier haplotypes) filter.sampleCount 1:35 filterByRange.sampleCount on filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on track hgsvc3Sv parent lrSv bigDataUrl /gbdb/$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=$geneCount filterValues.svType DEL,INS,DUP,INV,CPX filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:1321484 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:31711 filterByRange.insLen on filterLabel.insLen Insertion Length filter.geneCount 0:200 filterByRange.geneCount on filterLabel.geneCount Gene Count skipEmptyFields on + # NOT FOR RELEASE: data received from Eichler lab via email, not yet published. + # Do not add to lrSvAll merged track until a preprint or paper is available. + track lrSv1kLin + parent lrSv + bigDataUrl /gbdb/$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 +