44c00f07b0e94306e09f30c84ea6ab0f044e1a29 max Fri Aug 14 05:09:12 2026 -0700 adding lin et al long-read SV subtrack, refs #38099 diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index b19c31b037b..11a432fa725 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -17,123 +17,124 @@ 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 longReadVariants + priority 1 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) + longLabel Structural Variants from 1,427 CoLoRSdb samples (Consortium of Long-Read Sequencing, PacBio HiFi) type bigBed 9 + itemRgb on visibility hide dataVersion v1.2.0 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 (Hom $acHom, Het $acHet, Hemi $acHemi)<br><b>Samples</b>: $NS filterValues.svType DEL,INS,INV,DUP filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:101381 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:18724 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:2854 filterByRange.AC on filterLabel.AC Alt Allele Count (AC) filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 filterLabel.AF Allele Frequency (AF) skipEmptyFields on - priority 1 track lrSv1kgOnt parent longReadVariants + priority 4 bigDataUrl /gbdb/$D/lrSv/1kgOnt.bb - shortLabel 1KG ONT 1019 SVs - longLabel Structural Variants from 1000 Genomes Vienna ONT - 1,019 genomes (Schloissnig et al. 2025) + shortLabel 1KG Vienna ONT SVs + longLabel Structural Variants from 1,019 1000 Genomes samples (Vienna ONT; Schloissnig 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>Type</b>: $insType<br><b>Family</b>: $family<br><b>AC</b>: $AC<br><b>AF</b>: $alleleFreq filterValues.svType DEL,INS,CPX filterType.svType multipleListOr filterLabel.svType SV Type filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo filterType.insType multipleListOr filterLabel.insType Insertion/Deletion Type filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA filterType.family multipleListOr filterLabel.family Transposon Family filter.svLen 0:49171 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:48091 filterByRange.insLen on filterLabel.insLen Insertion Length filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:1816 filterByRange.AC on filterLabel.AC Allele Count skipEmptyFields on dataVersion 1.1 - priority 2 track gustafsonSv parent longReadVariants + priority 5 bigDataUrl /gbdb/$D/lrSv/gustafson.bb - shortLabel 1KG ONT UW 100 SVs - longLabel Structural Variants from 1000 Genomes University of Washington ONT - 100 samples (Gustafson et al. 2024) + shortLabel 1KG UW ONT SVs + longLabel Structural Variants from 100 1000 Genomes samples (University of Washington ONT; Gustafson et al. 2024) 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<br><b>Samples</b>: $sampleCount filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:98289 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:25094 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:200 filterByRange.AC on filterLabel.AC Allele Count (placeholder) filter.sampleCount 1:100 filterByRange.sampleCount on filterLabel.sampleCount Number of Carrier Samples skipEmptyFields on - priority 3 track noyvertSv parent longReadVariants + priority 6 bigDataUrl /gbdb/$D/lrSv/noyvert.bb - shortLabel 1KG ONT Boehringer - longLabel Structural Variants from 1000 Genomes ONT Boehringer - 888 Individuals (Noyvert et al. 2025) + shortLabel 1KG Boehringer ONT SVs + longLabel Structural Variants from 888 1000 Genomes samples (Boehringer ONT; 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>: ${nGwas} filterValues.svType DEL,INS,INV,DUP,BND filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:28634664 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:45109 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:1776 filterByRange.AC on @@ -165,34 +166,34 @@ filter.nGwas 0:11 filterByRange.nGwas on filterLabel.nGwas UK Biobank GWAS Hit Count filter.r2Loo 0:1 filterByRange.r2Loo on filterLimits.r2Loo 0:1 filterLabel.r2Loo Imputation r2 (leave-one-out) filter.concordanceLoo 0:1 filterByRange.concordanceLoo on filterLimits.concordanceLoo 0:1 filterLabel.concordanceLoo Minor Allele Concordance (leave-one-out) skipEmptyFields on track lrSv1kLin parent longReadVariants - release alpha + priority 3 bigDataUrl /gbdb/$D/lrSv/lin1218.bb - shortLabel 1KG Merged 1218 SVs - longLabel Structural Variants from 1000 Genomes merged - 1218 individuals (HiFi, ONT & assembly) + shortLabel 1KG Lin 1218 SVs + longLabel Structural Variants from 1,218 1000 Genomes samples (long-read merge; Lin et al.) 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>: $NS filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99565 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:99968 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:2436 filterByRange.AC on @@ -216,171 +217,177 @@ filter.afEur 0:1 filterByRange.afEur on filterLimits.afEur 0:1 filterLabel.afEur AF European filter.afSas 0:1 filterByRange.afSas on filterLimits.afSas 0:1 filterLabel.afSas AF South Asian filter.NS 1:1218 filterByRange.NS on filterLabel.NS Samples with Genotype Data skipEmptyFields on track aou1kSv parent longReadVariants + priority 2 bigDataUrl /gbdb/$D/lrSv/aou1k.bb shortLabel AoU 1027 SVs - longLabel Structural Variants from 1,027 AoU Individuals (PacBio HiFi Long-read) + longLabel Structural Variants from 1,027 All of Us samples (PacBio HiFi) 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 (approx)</b>: $AC<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:9905 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:9998 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:2054 filterByRange.AC on filterLabel.AC Allele Count (approx) filterByRange.afAfr on filterLimits.afAfr 0:1 filterLabel.afAfr AF African filterByRange.afEur on filterLimits.afEur 0:1 filterLabel.afEur AF European filterByRange.afEas on filterLimits.afEas 0:1 filterLabel.afEas AF East Asian skipEmptyFields on track han945Sv parent longReadVariants + priority 12 bigDataUrl /gbdb/$D/lrSv/han945.bb shortLabel Han 945 SVs - longLabel Structural Variants from 945 Han Chinese (Long-read Sequencing) + longLabel Structural Variants from 945 Han Chinese samples (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>AF</b>: $alleleFreq<br><b>AC</b>: $AC<br><b>Samples</b>: $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 longReadVariants + priority 14 bigDataUrl /gbdb/$D/lrSv/tommoJp.bb shortLabel ToMMo 333 SVs - longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios) + longLabel Structural Variants from 333 Japanese samples (ToMMo, 111 trios) 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>: $alleleFreq<br><b>AC</b>: $AC filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99985 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:30649 filterByRange.insLen on filterLabel.insLen Insertion Length filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:444 filterByRange.AC on filterLabel.AC Allele Count track ga4kSv parent longReadVariants + priority 16 bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb shortLabel GA4K 502 SVs - longLabel Structural Variants from 502 Children's Mercy GA4K Probands (PacBio HiFi) + longLabel Structural Variants from 502 GA4K samples (Children's Mercy, pediatric rare disease; PacBio HiFi) 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 (approx)</b>: $AC<br><b>AF</b>: $alleleFreq<br><b>Carriers</b>: $carrierCount/$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 longReadVariants + priority 11 bigDataUrl /gbdb/$D/lrSv/decodeSv.bb shortLabel deCODE 3622 SVs - longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore) + longLabel Structural Variants from 3,622 deCODE samples (Icelandic; Oxford Nanopore) type bigBed 9 + itemRgb on visibility hide mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen filterValues.svType DEL,INS,INSDEL filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:861080 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:22130 filterByRange.insLen on filterLabel.insLen Insertion Length skipEmptyFields on track hprc2v21Sv parent longReadVariants + priority 7 bigDataUrl /gbdb/$D/lrSv/hprc2v21.bb shortLabel HPRC v2.1 233 SVs - longLabel Structural Variants from HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus) + longLabel Structural Variants from 233 HPRC v2.1 assemblies (minigraph-cactus pangenome graph) 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>: $alleleFreq<br><b>AC</b>: $AC/$alleleNumber<br><b>Samples</b>: $nSamples filterValues.svType INS,DEL filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99835 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:1064897 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:463 filterByRange.AC on @@ -424,66 +431,68 @@ #filterLimits.alleleFreq 0:1 #filterLabel.alleleFreq Carrier Frequency #filter.nCallers 1:14 #filterByRange.nCallers on #filterLabel.nCallers Number of Supporting Callers #filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish #filterType.callers multipleListAnd #filterLabel.callers Supporting Callers #filterValues.sources PAV,dipcall,longcallD #filterType.sources multipleListAnd #filterLabel.sources Source Pipeline #skipEmptyFields on track hgsvc2Sv parent longReadVariants + priority 9 bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb shortLabel HGSVC2 32 SVs - longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert 2021) + longLabel Structural Variants from 32 HGSVC2 assemblies (freeze 4; Ebert et al. 2021) 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>Samples</b>: $sampleCount<br><b>AC</b>: $AC<br><b>AF</b>: $popAllAf filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:57207414 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:108546 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 1:35 filterByRange.AC on filterLabel.AC Allele Count (carrier haplotypes) filter.sampleCount 1:35 filterByRange.sampleCount on filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on track hgsvc3Sv parent longReadVariants + priority 8 bigDataUrl /gbdb/$D/lrSv/hgsvc3.bb shortLabel HGSVC3 65 SVs - longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI) + longLabel Structural Variants from 65 HGSVC3 assemblies (diverse ancestry; HiFi + ONT) 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>Samples</b>: $sampleCount<br><b>AC</b>: $AC filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:30176500 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:30176500 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 1:136 filterByRange.AC on @@ -537,108 +546,112 @@ filterByRange.afHc on filterLimits.afHc 0:1 filterLabel.afHc Allele Frequency (HC) filter.afIlbd 0:1 filterByRange.afIlbd on filterLimits.afIlbd 0:1 filterLabel.afIlbd Allele Frequency (ILBD) filter.differentialRate -1:1 filterByRange.differentialRate on filterLimits.differentialRate -1:1 filterLabel.differentialRate Case-Control Differential (case - control) skipEmptyFields on track aprSv parent longReadVariants + priority 15 bigDataUrl /gbdb/$D/lrSv/apr.bb shortLabel Arab APR 53 SVs - longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples) + longLabel Structural Variants from 53 Arab Pangenome Reference samples (UAE-resident; HiFi + ONT) 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>: $AC/$alleleNumber<br><b>AF</b>: $alleleFreq<br><b>Samples</b>: $numSamples<br><b>Alts</b>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99885 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:584016 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:107 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track cpc1Sv parent longReadVariants + priority 13 bigDataUrl /gbdb/$D/lrSv/cpc1.bb shortLabel CPC 58 SVs - longLabel Structural Variants from the Chinese Pangenome Consortium (58 samples, CPC-only) + longLabel Structural Variants from 58 Chinese Pangenome Consortium samples (CPC-only; HiFi) 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>: $AC/$alleleNumber<br><b>AF</b>: $alleleFreq<br><b>Samples</b>: $numSamples<br><b>Alts</b>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:8998096 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:376583 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:116 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track chirmade101Sv parent longReadVariants + priority 17 bigDataUrl /gbdb/$D/lrSv/chirmade101.bb shortLabel SVatalog 101 SVs - longLabel Structural Variants from 101 Long-read WGS (GWAS SVatalog, Chirmade 2026) + longLabel Structural Variants from 101 SVatalog samples (cystic fibrosis; Chirmade et al. 2026) 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>Genes</b>: $geneCount filterValues.svType DEL,INS,DUP,INV,CPX filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:1321484 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:31711 filterByRange.insLen on filterLabel.insLen Insertion Length filter.geneCount 0:200 filterByRange.geneCount on filterLabel.geneCount Gene Count skipEmptyFields on track cardSv parent longReadVariants + priority 10 bigDataUrl /gbdb/$D/lrSv/card.bb shortLabel CARD 351 SVs - longLabel Structural Variants from 351 Brain Samples (NIH CARD Long-read ONT, NABEC + HBCC) + longLabel Structural Variants from 351 NIH CARD brain samples (ONT; NABEC + HBCC) 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>: ${alleleFreq}<br><b>AC</b>: ${AC} (NABEC ${nabecAc}, HBCC ${hbccAc}) filterValues.svType DEL,INS,INV,DUP filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:30282742 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:92867161 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:702 filterByRange.AC on