526213b2893134217a300ff913e11b4e98d67991 max Mon Apr 20 08:50:10 2026 -0700 lrSv: add cpc1Sv and aprSv pangenome SV subtracks (hg38, hs1) cpc1Sv: 97,205 SVs from the CPC + HPRC Phase 1 pangenome (Gao et al 2023, Nature; PMID 37316654) built on T2T-CHM13v2, with 53 Chinese and 47 HPRC samples. Each graph snarl site is shown as one item with alt alleles classified by length delta (INS/DEL/CPX, 50 bp threshold) and collapsed. aprSv: 103,077 SVs from the Arabic Pangenome Reference (Nassir et al. 2025, Nat Commun; PMID 40707445) built on T2T-CHM13v2 from 53 UAE-resident Arab individuals. Same multi-allele classification as cpc1Sv, with alt alleles iterated within each multi-allelic row. Both tracks load natively on hs1 and are lifted to hg38 with hs1ToHg38.over.chain.gz. refs #36258 diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index d913600e518..f51bf6bfca1 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -1,126 +1,203 @@ track lrSv superTrack on shortLabel Long-read SVs longLabel Structural Variants from Long-read Sequencing group varRep visibility hide - track han945Sv + track colorsDbSv parent lrSv - bigDataUrl /gbdb/$D/lrSv/han945.bb - shortLabel Han 945 SVs - longLabel Structural Variants from 945 Han Chinese (Long-read Sequencing) + bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb + shortLabel CoLoRSdb 1,427 SVs + longLabel Structural Variants from CoLoRSdb (Consortium of Long-Read Sequencing, 1,427 Samples) type bigBed 9 + itemRgb on visibility dense - mouseOver <b>$name</b> ($svType) len=$svLen AF=$alleleFreq samples=$sampleCount - filterValues.svType DEL,INS,DUP,INV,TRA + 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 0:99743 + filter.svLen 20:101381 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 + filter.AC 0:2854 + filterByRange.AC on + filterLabel.AC Alt Allele Count (AC) skipEmptyFields on - urls chr2="hgTracks?position=$$" + priority 1 track lrSv1kgOnt parent lrSv bigDataUrl /gbdb/$D/lrSv/1kgOnt.bb - shortLabel 1KG ONT SVs - longLabel Structural Variants from 1,019 Diverse Humans (1000 Genomes ONT) + 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 tommoJpSv + track onekg3202Sr parent lrSv - bigDataUrl /gbdb/$D/lrSv/tommoJp.bb - shortLabel ToMMo Japanese SVs - longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios) + 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 - filterValues.svType DEL,INS + 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 51:99980 + 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 - filter.alleleCount 0:444 - filterByRange.alleleCount on - filterLabel.alleleCount Allele Count + 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 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/$sampleTotal filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:809711 filterByRange.svLen on filterLabel.svLen SV Length @@ -137,35 +214,89 @@ bigDataUrl /gbdb/$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/$D/lrSv/hgsvc3.bb shortLabel HGSVC3 65 SVs - longLabel Structural Variants from 65 Diverse Samples (HGSVC3, Haplotype-Resolved Long-read Assemblies) + longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$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 @@ -203,30 +334,72 @@ 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+HPRC 105 SVs + longLabel Structural Variants from CPC + HPRC Phase 1 Pangenome (105 samples, 58 Chinese + 47 HPRC) + 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