f058c8fe4601b223ff47468eb3525c05ccd03850 max Wed Apr 22 09:17:17 2026 -0700 srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258 diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index 2f553ecbf1e..777dc5bd0bd 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -1,584 +1,470 @@ 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,INS,INV,CPX,DUP,CNV,CTX,INSDEL,MIXED,BND,MEI,TRA 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 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=$alleleFreq filterValues.svType DEL,INS,CPX filterType.svType multipleListOr filterLabel.svType SV Type filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo filterType.insType multipleListOr filterLabel.insType Insertion/Deletion Type filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA filterType.family multipleListOr filterLabel.family Transposon Family filter.svLen 0:49171 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:48091 filterByRange.insLen on filterLabel.insLen Insertion Length filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:1816 filterByRange.AC on filterLabel.AC Allele Count skipEmptyFields on dataVersion 1.1 priority 2 - track abelSv - parent lrSv - bigDataUrl /gbdb/$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) svLen=$svLen insLen=$insLen AF=$af AC=$AC/$an callset=$callset MSQ=$msq - skipEmptyFields on - skipFields mateChrom,matePos - filterValues.svType DEL|deletion,DUP|duplication,INV|inversion,MEI|mobile element insertion,BND|breakend/translocation - filterType.svType multipleListOr - filterLabel.svType SV Type - filterValues.callset B38|Native GRCh38 callset (14623 samples),B37lift|Lifted from GRCh37 callset (8417 samples) - filterType.callset multipleListOr - filterLabel.callset Source Callset - filterValues.filter PASS|High confidence,LOW|Low confidence - filterType.filter multipleListOr - filterLabel.filter Filter Status - filterByRange.af on - filter.af 0:1 - filterLimits.af 0:1 - filterLabel.af Allele Frequency (AF) - filterByRange.svLen on - filter.svLen 0:250000000 - filterLimits.svLen -1:250000000 - filterLabel.svLen SV Length (bp; -1 for BND) - filter.insLen 0:8545 - filterByRange.insLen on - filterLabel.insLen Insertion Length - filterByRange.msq on - filter.msq 0:500 - filterLimits.msq 0:500 - filterLabel.msq Mean Sample Quality (MSQ) - filterByRange.AC on - filter.AC 0:30000 - filterLimits.AC 0:30000 - filterLabel.AC Allele Count (AC) - url https://www.nature.com/articles/s41586-020-2371-0 - urlLabel Abel et al, Nature 2020: - - track onekg3202Sr - parent lrSv - bigDataUrl /gbdb/$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) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber popMax=$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.insLen 0:178243 - filterByRange.insLen on - filterLabel.insLen Insertion Length - filter.AC 0:6404 - filterByRange.AC on - filterLabel.AC Allele Count - 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> ($svType) svLen=$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 tommoJpCnv - parent lrSv - container multiWig - aggregate transparentOverlay - showSubtrackColorOnUi on - shortLabel ToMMo 48K CNV SR - longLabel CNV Carrier Counts from 48,874 Japanese Individuals (ToMMo 48KJPN-CNV, short-read WGS; 1 kb bins) - included for comparison - type bigWig 0 48874 - autoScale on - viewLimits 0:1000 - viewLimitsMax 0:48874 - maxHeightPixels 100:32:8 - visibility full - priority 2.5 - - track tommoJpCnvLoss - parent tommoJpCnv - bigDataUrl /gbdb/$D/lrSv/tommoJpCnvLoss.bw - shortLabel ToMMo CNV Loss - longLabel Samples with copy-number loss (CN<2) per 1 kb bin, ToMMo 48KJPN-CNV - type bigWig 0 48874 - color 200,0,0 - altColor 200,0,0 - - track tommoJpCnvGain - parent tommoJpCnv - bigDataUrl /gbdb/$D/lrSv/tommoJpCnvGain.bw - shortLabel ToMMo CNV Gain - longLabel Samples with copy-number gain (CN>2) per 1 kb bin, ToMMo 48KJPN-CNV - type bigWig 0 48874 - color 0,160,0 - altColor 0,160,0 - 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=$nSamples filterValues.svType INS,DEL,CPX,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99113 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:97718 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:463 filterByRange.AC on filterLabel.AC Allele Count filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.snarlLevel 0:10 filterByRange.snarlLevel on filterLabel.snarlLevel Snarl Level skipEmptyFields on track hgsvc2Sv parent lrSv bigDataUrl /gbdb/$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