151410cc48b9b1f8b1cb9bee89b7004eca871c61 max Wed Apr 22 09:03:35 2026 -0700 lrSv: harmonize long-read shortLabels, add aprSv/cpc1Sv/abelSv to overview Normalize the shortLabel text of every long-read subtrack to the pattern "<Cohort> <N> SVs" (no commas in N): CoLoRSdb 1427, AoU 1027, ToMMo 333, GA4K 502, deCODE 3622, HPRC v2 233, Kim PD 100 prelim. Short-read comparators (abelSv, onekg3202Sr, tommoJpCnv) are left alone per user instruction. Also add three rows that were missing from lrSv.html's overview table: aprSv (Arab APR 53), cpc1Sv (CPC 58, HPRC-specific SVs removed) and abelSv (CCDG 17,795 Illumina short-read comparator). Updates the comparator footnote to mention both short-read rows. refs #36258 diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index a1fd5e56ed5..2f553ecbf1e 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -14,31 +14,31 @@ 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 1,427 SVs + 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=$NS searchIndex name filterValues.svType DEL,INS,INV,DUP filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:101381 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:18724 filterByRange.insLen on @@ -186,31 +186,31 @@ filter.insLen 0:25094 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:200 filterByRange.AC on filterLabel.AC Allele Count (placeholder) filter.sampleCount 1:100 filterByRange.sampleCount on filterLabel.sampleCount Number of Carrier Samples skipEmptyFields on priority 3 track aou1kSv parent lrSv bigDataUrl /gbdb/$D/lrSv/aou1k.bb - shortLabel AoU 1K SVs + 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=$afEur filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:9905 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:9998 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:2054 @@ -282,109 +282,109 @@ color 200,0,0 altColor 200,0,0 track tommoJpCnvGain parent tommoJpCnv bigDataUrl /gbdb/$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/$D/lrSv/tommoJp.bb - shortLabel ToMMo Japanese SVs + shortLabel ToMMo 333 SVs longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$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 SVs + 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/$D/lrSv/decodeSv.bb - shortLabel deCODE 3,622 SVs + shortLabel deCODE 3622 SVs longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$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/$D/lrSv/hprc2.bb - shortLabel HPRC v2 SVs + shortLabel HPRC v2 233 SVs longLabel Structural Variants from the HPRC v2 Pangenome Graph (233 Samples, minigraph-cactus + vcfwave) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber samples=$nSamples filterValues.svType INS,DEL,CPX,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99113 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:97718 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:463 @@ -456,31 +456,31 @@ filter.sampleCount 1:65 filterByRange.sampleCount on filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on track kwanhoSv parent lrSv bigDataUrl /gbdb/$D/lrSv/kwanho.bb - shortLabel Kim PD Brain SVs (preliminary) + 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