7594507ca126d5242346787e42e13c52ea7709b1 max Fri Apr 17 08:40:31 2026 -0700 Add lrSv supertrack: long-read structural variants from 9 studies (hg38). #Preview2 week - bugs introduced now will need a build patch to fix Sub-tracks (all bigBed 9+): han945Sv - 945 Han Chinese, ONT (Gong 2025, PMID 39929826) lrSv1kgOnt - 1019 1000 Genomes, ONT, SVAN-annotated (Schloissnig 2025, PMID 40702182; lifted from hs1) tommoJpSv - 333 Japanese (111 trios), ONT (Otsuki 2022, PMID 36127505) aou1kSv - 1027 All of Us, PacBio HiFi (Garimella 2025, PMID 41256123) ga4kSv - 502 GA4K pediatric rare disease, PacBio HiFi (Cohen 2022, PMID 35305867) decodeSv - 3622 Icelanders, ONT (Beyter 2021, PMID 33972781) hgsvc3Sv - 65 HGSVC3 diverse haplotype-resolved assemblies, HiFi+ONT (Logsdon 2025, PMID 40702183; merges insdel+inv tables) kwanhoSv - 100 post-mortem brains (PD/ILBD/HC), PacBio HiFi (Kim 2026, PMID 41929179) chirmade101Sv - 101 long-read WGS GWAS SVatalog cohort (Chirmade 2026, PMID 41203876) Includes per-track conversion scripts and autoSql under scripts/lrSv/, the supertrack summary table in lrSv.html, and a consolidated makeDoc at doc/hg38/lrSv.txt. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index ca1304a9380..d913600e518 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -97,15 +97,141 @@ 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 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=$svLen + filterValues.svType DEL,INS,INSDEL + filterType.svType multipleListOr + filterLabel.svType SV Type + filter.svLen 0:861080 + filterByRange.svLen on + filterLabel.svLen SV Length + skipEmptyFields on + + track hgsvc3Sv + parent lrSv + bigDataUrl /gbdb/$D/lrSv/hgsvc3.bb + shortLabel HGSVC3 65 SVs + longLabel Structural Variants from 65 Diverse Samples (HGSVC3, Haplotype-Resolved Long-read Assemblies) + 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 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 +