ae2a62a18bf9750819f17f8f2237b1f7b1b9911f lrnassar Sat Jun 13 10:48:41 2026 -0700 lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258 Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept), and remove the searchIndex name settings that were added by mistake. searchIndex removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll rebuild will drop KimPD from databases.tsv / the merged track. diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index 6d1d9eff546..60da0554002 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -23,31 +23,30 @@ filterLabel.AC Allele Count noScoreFilter on include lrSvAll.ra 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=$NS - searchIndex name filterValues.svType DEL,INS,INV,DUP filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:101381 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:18724 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:2854 filterByRange.AC on filterLabel.AC Alt Allele Count (AC) filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 @@ -381,71 +380,77 @@ filter.AC 1:136 filterByRange.AC on filterLabel.AC Allele Count (carrier haplotypes) filter.sampleCount 1:65 filterByRange.sampleCount on filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on - track kwanhoSv - parent lrSv - bigDataUrl /gbdb/$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 + # kwanhoSv commented out: the Kim PD brain callset is preliminary and + # unpublished (the description page says do not release until publication), + # and carries breakend artifacts up to ~190 Mb. Held off dev/alpha until a + # paper is out. bigBed, .as, converter and makeDoc are retained. The + # pending lrSvAll rebuild will also drop KimPD from databases.tsv so it + # leaves the merged track. refs #36258 + #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 the Arab 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=$numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99885 filterByRange.svLen on @@ -509,31 +514,30 @@ filterByRange.geneCount on filterLabel.geneCount Gene Count skipEmptyFields on # NOT FOR RELEASE: data received from Eichler lab via email, not yet published. # Do not add to lrSvAll merged track until a preprint or paper is available. track lrSv1kLin parent lrSv bigDataUrl /gbdb/$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 dense mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$AN AF=$AF AF_AFR=$afAfr AF_EUR=$afEur samples=$NS - searchIndex name 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 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