65091fe6f6487c23d650a144e947fc1c582d3f40 max Tue Apr 21 02:16:16 2026 -0700 abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376 diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index f51bf6bfca1..808454bdf4b 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -1,410 +1,449 @@ 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 mouseOver <b>$name</b> ($svType) len=$svLen AF=$af AC=$AC (Hom:$AC_Hom Het:$AC_Het Hemi:$AC_Hemi) samples=$NS searchIndex name filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 20:101381 filterByRange.svLen on filterLabel.svLen SV Length filter.AC 0:2854 filterByRange.AC on filterLabel.AC Alt Allele Count (AC) skipEmptyFields on priority 1 track lrSv1kgOnt parent lrSv bigDataUrl /gbdb/$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 <b>$name</b> ($svClass) len=$svLen type=$insType family=$family AC=$alleleCount AF=$alleleFreq filterValues.svClass DEL,INS,COMPLEX filterType.svClass multipleListOr filterLabel.svClass SV Class filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo filterType.insType multipleListOr filterLabel.insType Insertion/Deletion Type filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA filterType.family multipleListOr filterLabel.family Transposon Family filterByRange.svLen on filterLabel.svLen SV Length filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filterByRange.alleleCount on filterLabel.alleleCount Allele Count skipEmptyFields on priority 2 + track abelSv + parent lrSv + bigDataUrl /gbdb/$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) 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/$D/lrSv/onekg3202sr.bb shortLabel 1KG 3202 SR SVs longLabel 1000 Genomes 3202-sample Illumina SHORT-READ GATK-SV callset (Byrska-Bishop 2022) - included for comparison type bigBed 9 + itemRgb on visibility dense mouseOver <b>$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 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/$D/lrSv/gustafson.bb shortLabel 1KG ONT 100 SVs longLabel Structural Variants from 100 1000 Genomes ONT Samples (Gustafson et al. 2024) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$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/$sampleTotal filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:809711 filterByRange.svLen on filterLabel.svLen SV Length filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.carrierCount 1:498 filterByRange.carrierCount on filterLabel.carrierCount Number of Carrier Samples track decodeSv parent lrSv bigDataUrl /gbdb/$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 <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/$D/lrSv/hgsvc3.bb shortLabel HGSVC3 65 SVs longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$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 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/$D/lrSv/kwanho.bb shortLabel Kim PD Brain SVs longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$name</b> ($svType) len=$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 <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 filter.geneCount 0:200 filterByRange.geneCount on filterLabel.geneCount Gene Count skipEmptyFields on