e6bcec351aa8f5bc7218e8862e15c149aadb3479 lrnassar Fri Jul 10 12:18:40 2026 -0700 lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged. diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index 2873d0e21c5..7bcce88a09c 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -1,73 +1,74 @@ -track lrSv +track longReadVariants superTrack on shortLabel Long-read SVs longLabel Structural Variants from Long-read Sequencing +html lrSv group varRep visibility hide # Supertrack-level filters. These are rendered on the supertrack's own # hgTrackUi page (superTrackUi in hgTrackUi.c). Cart values stored under # "lrSv.filter.<field>.min/max" are inherited at read time by every # subtrack via cartOptionalStringClosestToHome() walking tdb->parent. A # subtrack-level filter always wins over the supertrack-level one. filterValues.svType DEL|DEL (Deletion),INS|INS (Insertion),INV|INV (Inversion),CPX|CPX (Complex rearrangement),DUP|DUP (Duplication),INSDEL|INSDEL (Insertion-deletion),MIXED|MIXED (multi-allele snarl),TRA|TRA (Translocation) filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:250000000 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:30176500 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:30000 filterByRange.AC on filterLabel.AC Allele Count noScoreFilter on include lrSvAll.ra track colorsDbSv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$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 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>: $NS filterValues.svType DEL,INS,INV,DUP filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:101381 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:18724 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:2854 filterByRange.AC on filterLabel.AC Alt Allele Count (AC) filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 filterLabel.AF Allele Frequency (AF) skipEmptyFields on priority 1 track lrSv1kgOnt - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$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 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>: $alleleFreq filterValues.svType DEL,INS,CPX filterType.svType multipleListOr filterLabel.svType SV Type filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo filterType.insType multipleListOr filterLabel.insType Insertion/Deletion Type filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA filterType.family multipleListOr @@ -77,58 +78,58 @@ filterLabel.svLen SV Length filter.insLen 0:48091 filterByRange.insLen on filterLabel.insLen Insertion Length filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:1816 filterByRange.AC on filterLabel.AC Allele Count skipEmptyFields on dataVersion 1.1 priority 2 track gustafsonSv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$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 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>: $sampleCount filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:98289 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:25094 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:200 filterByRange.AC on filterLabel.AC Allele Count (placeholder) filter.sampleCount 1:100 filterByRange.sampleCount on filterLabel.sampleCount Number of Carrier Samples skipEmptyFields on priority 3 track aou1kSv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$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 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>: $afEur filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:9905 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:9998 filterByRange.insLen on @@ -136,137 +137,137 @@ filter.AC 0:2054 filterByRange.AC on filterLabel.AC Allele Count (approx) filterByRange.afAfr on filterLimits.afAfr 0:1 filterLabel.afAfr AF African filterByRange.afEur on filterLimits.afEur 0:1 filterLabel.afEur AF European filterByRange.afEas on filterLimits.afEas 0:1 filterLabel.afEas AF East Asian skipEmptyFields on track han945Sv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/han945.bb shortLabel Han 945 SVs longLabel Structural Variants from 945 Han Chinese (Long-read Sequencing) type bigBed 9 + itemRgb on visibility 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 lrSv + parent longReadVariants 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 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>: $AC filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99985 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:30649 filterByRange.insLen on filterLabel.insLen Insertion Length filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:444 filterByRange.AC on filterLabel.AC Allele Count track ga4kSv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb shortLabel GA4K 502 SVs longLabel Structural Variants from 502 Children's Mercy GA4K Probands (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 lrSv + parent longReadVariants 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 hide mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen filterValues.svType DEL,INS,INSDEL filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:861080 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:22130 filterByRange.insLen on filterLabel.insLen Insertion Length skipEmptyFields on track hprc2v21Sv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/hprc2v21.bb shortLabel HPRC v2.1 233 SVs longLabel Structural Variants from HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus) 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>: $nSamples filterValues.svType INS,DEL filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99835 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:1064897 filterByRange.insLen on @@ -276,31 +277,31 @@ filterLabel.AC Allele Count filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.snarlLevel 0:7 filterByRange.snarlLevel on filterLabel.snarlLevel Snarl Level skipEmptyFields on # hprc2JasmineSv commented out: the Jasmine-merged HPRC v2 multi-caller # set is a test/comparison callset (the Hall lab is not happy with it) and # is not for release. bigBed, .as, converter and makeDoc are retained. # refs #36258 #track hprc2JasmineSv - #parent lrSv + #parent longReadVariants #bigDataUrl /gbdb/$D/lrSv/hprc2Jasmine.bb #shortLabel HPRC2 Jasmine 231 SVs #longLabel Structural Variants from 231 HPRC v2 Assemblies (Jasmine merge of 14 SV callers) #type bigBed 9 + #itemRgb on #visibility dense #mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$nSamples/$alleleNumber AF=$alleleFreq callers=$nCallers ($callers) #filterValues.svType DEL,INS #filterType.svType multipleListOr #filterLabel.svType SV Type #filter.svLen 0:30176500 #filterByRange.svLen on #filterLabel.svLen SV Length #filter.insLen 0:30176500 #filterByRange.insLen on @@ -312,31 +313,31 @@ #filterByRange.alleleFreq on #filterLimits.alleleFreq 0:1 #filterLabel.alleleFreq Carrier Frequency #filter.nCallers 1:14 #filterByRange.nCallers on #filterLabel.nCallers Number of Supporting Callers #filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish #filterType.callers multipleListAnd #filterLabel.callers Supporting Callers #filterValues.sources PAV,dipcall,longcallD #filterType.sources multipleListAnd #filterLabel.sources Source Pipeline #skipEmptyFields on track hgsvc2Sv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb shortLabel HGSVC2 32 SVs longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert 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>: $popAllAf filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:57207414 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:108546 filterByRange.insLen on @@ -345,31 +346,31 @@ filterByRange.AC on filterLabel.AC Allele Count (carrier haplotypes) filter.sampleCount 1:35 filterByRange.sampleCount on filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on track hgsvc3Sv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/hgsvc3.bb shortLabel HGSVC3 65 SVs longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI) type bigBed 9 + itemRgb on visibility 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>: $AC filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:30176500 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:30176500 filterByRange.insLen on @@ -382,31 +383,31 @@ filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on # NOT FOR RELEASE: preliminary and unpublished (Kim et al. 2026 not out yet), # and the callset has breakend artifacts up to 190 Mb (e.g. a single "INV" # spanning all of chr4). Held on dev/alpha and kept out of the lrSvAll merge # (removed from databases.tsv) until the data is published and cleaned. track kwanhoSv - parent lrSv + parent longReadVariants release alpha bigDataUrl /gbdb/$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>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC<br><b>AF (PD)</b>: $afPd<br><b>AF (HC)</b>: $afHc<br><b>Case-control diff</b>: $differentialRate filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:200000000 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:20145 @@ -425,108 +426,108 @@ filter.afHc 0:1 filterByRange.afHc on filterLimits.afHc 0:1 filterLabel.afHc Allele Frequency (HC) filter.afIlbd 0:1 filterByRange.afIlbd on filterLimits.afIlbd 0:1 filterLabel.afIlbd Allele Frequency (ILBD) filter.differentialRate -1:1 filterByRange.differentialRate on filterLimits.differentialRate -1:1 filterLabel.differentialRate Case-Control Differential (case - control) skipEmptyFields on track aprSv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/apr.bb shortLabel Arab APR 53 SVs longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples) 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>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99885 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:584016 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:107 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track cpc1Sv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/cpc1.bb shortLabel CPC 58 SVs longLabel Structural Variants from the Chinese Pangenome Consortium (58 samples, CPC-only) 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>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:8998096 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:376583 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:116 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track chirmade101Sv - parent lrSv + parent longReadVariants bigDataUrl /gbdb/$D/lrSv/chirmade101.bb shortLabel SVatalog 101 SVs longLabel Structural Variants from 101 Long-read WGS (GWAS SVatalog, Chirmade 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>: $geneCount filterValues.svType DEL,INS,DUP,INV,CPX filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:1321484 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:31711 filterByRange.insLen on filterLabel.insLen Insertion Length filter.geneCount 0:200 filterByRange.geneCount on filterLabel.geneCount Gene Count skipEmptyFields on # NOT FOR RELEASE: data received from Eichler lab via email, not yet published. # Do not add to lrSvAll merged track until a preprint or paper is available. track lrSv1kLin - parent lrSv + parent longReadVariants release alpha bigDataUrl /gbdb/$D/lrSv/lin1218.bb shortLabel 1KG Linear 1218 SVs longLabel Structural Variants from 1,218 Individuals (1000 Genomes, Linear 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>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