b687dd9018670941ce30f8a4582d6597c5a974d8 lrnassar Tue Sep 1 14:57:43 2026 -0700 lrSv1kLin: fix 2bp insertion span, drop dead numConsolidated field, refresh lrSvAll merge. refs #38099 The Lin 1218 VCFs set INFO/END = POS+1 on insertions, and the converter took chromEnd from END, so every insertion was drawn 2bp wide with svLen 2 instead of the 1bp anchor base. That contradicted the track's own description page and the coordinate convention in the makeDoc, and it kept 107,980 Lin insertions from merging in lrSvAll. Insertions now clamp chromEnd to the anchor; deletions are unchanged and still verify span == |SVLEN| against the source VCFs. Dropped numConsolidated from the converter and the .as: the NumConsolidated INFO key is declared in the VCF header but never appears on a data line, so the column was 0 on all 1.2M rows and added a meaningless line to every detail page. Rebuilt lin1218 on hg38 and hs1 (item counts and variant names unchanged) and re-ran the merge: lrSvAll 2,963,093 -> 2,855,267 rows as the duplicate insertion rows collapse. Bumped seven filter.svLen/insLen maxima in lrSv.ra that were short of the data after the August deletion narrowing, three of them only visible on hs1. lrSvAll.html said the 1000 Genomes linear set was not in the merge, which is no longer true, and gave no warning that sourceCount double-counts because Lin1218 already absorbs HPRC, HGSVC3 and both 1KG ONT callsets. Corrected the merge key description and refreshed ten stale cells in the lrSv.html summary table. diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index 11a432fa725..c8265b73f02 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -29,31 +29,31 @@ track colorsDbSv parent longReadVariants priority 1 bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb shortLabel CoLoRSdb 1427 SVs longLabel Structural Variants from 1,427 CoLoRSdb samples (Consortium of Long-Read Sequencing, PacBio HiFi) 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>: $NS filterValues.svType DEL,INS,INV,DUP filterType.svType multipleListOr filterLabel.svType SV Type - filter.svLen 0:101381 + filter.svLen 0:111110 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:18724 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:2854 filterByRange.AC on filterLabel.AC Alt Allele Count (AC) filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 filterLabel.AF Allele Frequency (AF) skipEmptyFields on track lrSv1kgOnt @@ -91,31 +91,31 @@ dataVersion 1.1 track gustafsonSv parent longReadVariants priority 5 bigDataUrl /gbdb/$D/lrSv/gustafson.bb shortLabel 1KG UW ONT SVs longLabel Structural Variants from 100 1000 Genomes samples (University of Washington ONT; 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>: $sampleCount filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type - filter.svLen 0:98289 + filter.svLen 0:98290 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:25094 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:200 filterByRange.AC on filterLabel.AC Allele Count (placeholder) filter.sampleCount 1:100 filterByRange.sampleCount on filterLabel.sampleCount Number of Carrier Samples skipEmptyFields on track noyvertSv parent longReadVariants @@ -177,31 +177,31 @@ skipEmptyFields on track lrSv1kLin parent longReadVariants priority 3 bigDataUrl /gbdb/$D/lrSv/lin1218.bb shortLabel 1KG Lin 1218 SVs longLabel Structural Variants from 1,218 1000 Genomes samples (long-read merge; Lin et al.) 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>: $NS filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type - filter.svLen 0:99565 + filter.svLen 0:99691 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:99968 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:2436 filterByRange.AC on filterLabel.AC Allele Count filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 filterLabel.AF Allele Frequency filter.afAfr 0:1 filterByRange.afAfr on filterLimits.afAfr 0:1 @@ -261,31 +261,31 @@ skipEmptyFields on track han945Sv parent longReadVariants priority 12 bigDataUrl /gbdb/$D/lrSv/han945.bb shortLabel Han 945 SVs longLabel Structural Variants from 945 Han Chinese samples (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>AF</b>: $alleleFreq<br><b>AC</b>: $AC<br><b>Samples</b>: $sampleCount filterValues.svType DEL,INS,DUP,INV,TRA filterType.svType multipleListOr filterLabel.svType SV Type - filter.svLen 0:99743 + filter.svLen 0:99744 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:27242 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:1890 filterByRange.AC on filterLabel.AC Allele Count (approx 2*SUPP) filter.sampleCount 1:945 filterByRange.sampleCount on filterLabel.sampleCount Number of Supporting Samples filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency @@ -320,31 +320,31 @@ filterLabel.AC Allele Count track ga4kSv parent longReadVariants priority 16 bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb shortLabel GA4K 502 SVs longLabel Structural Variants from 502 GA4K samples (Children's Mercy, pediatric rare disease; 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 + filter.svLen 0:809712 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 @@ -557,61 +557,61 @@ skipEmptyFields on track aprSv parent longReadVariants priority 15 bigDataUrl /gbdb/$D/lrSv/apr.bb shortLabel Arab APR 53 SVs longLabel Structural Variants from 53 Arab Pangenome Reference samples (UAE-resident; HiFi + ONT) 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>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type - filter.svLen 0:99885 + filter.svLen 0:99892 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:584016 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:107 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track cpc1Sv parent longReadVariants priority 13 bigDataUrl /gbdb/$D/lrSv/cpc1.bb shortLabel CPC 58 SVs longLabel Structural Variants from 58 Chinese Pangenome Consortium samples (CPC-only; 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</b>: $AC/$alleleNumber<br><b>AF</b>: $alleleFreq<br><b>Samples</b>: $numSamples<br><b>Alts</b>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:8998096 filterByRange.svLen on filterLabel.svLen SV Length - filter.insLen 0:376583 + filter.insLen 0:414249 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:116 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track chirmade101Sv parent longReadVariants priority 17 bigDataUrl /gbdb/$D/lrSv/chirmade101.bb shortLabel SVatalog 101 SVs