f4d967492fedb59d2e528cf196e35c1da248ae96 lrnassar Fri Oct 2 07:15:47 2026 -0700 Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM. diff --git src/hg/makeDb/trackDb/human/strVarNew.ra src/hg/makeDb/trackDb/human/strVarNew.ra index 2685250b80c..822957585b2 100644 --- src/hg/makeDb/trackDb/human/strVarNew.ra +++ src/hg/makeDb/trackDb/human/strVarNew.ra @@ -1,125 +1,124 @@ # Tandem Repeat Variation, shared by all human assemblies. # # ALPHA ONLY, ON PURPOSE. This is the version that follows STRchive's GitHub # releases and puts the track on hg19 and hs1. It is held back from beta and # public until the sysadmins install the strchiveAutoPush cron (see # kent/src/hg/utils/otto/strchive/strchiveAutoPush and #38268) -- without that # push, the RR would advertise data it does not have. hg38/strVar.ra is the # released version and is tagged beta,public so the two never overlap. # # TO RELEASE, once the auto-push is running: # - drop the "alpha" from "include strVarNew.ra alpha" in human/trackDb.ra # - delete human/hg38/strVar.ra, strVar.html and strchive.html, and the # "include strVar.ra beta,public" line in human/hg38/trackDb.ra # - rename strVarNew.ra/.html and strchiveNew.html back to strVar/strchive # and drop the "html strVarNew" / "html strchiveNew" lines below # # The bigDataUrls use $D rather than a hardcoded assembly, and hgTrackDb -strict # drops any track whose bigDataUrl file is not there. So a member appears only on # the assemblies it was actually built for: today STRchive is on hg19, hg38 and hs1 # and the rest are hg38-only. To add a member on another assembly, put the file in # /gbdb/<db>/strVar/ and rebuild trackDb -- nothing here needs to change. track strVar html strVarNew shortLabel Tandem Repeat Variation longLabel Tandem Repeat Variation group varRep superTrack on visibility hide -pennantIcon New red ../goldenPath/newsarch.html#041026 "Released Apr. 10, 2026" track webstr shortLabel WebSTR longLabel WebSTR Short Tandem Repeat Loci (EnsembleTR Panel, 1000 Genomes) type bigBed 9 + itemRgb on bigDataUrl /gbdb/$D/strVar/webstr.bb visibility dense superTrack strVar dense # hg38 is not $D here on purpose: this is WebSTR's own url and we only built # this track for hg38, so it is the only assembly where the track shows up urls repeatId="https://webstr.ucsd.edu/locus?repeat_id=$$&genome=hg38" url https://webstr.ucsd.edu/locus?repeat_id=$<repeatId>&genome=hg38 urlLabel Link to repeat record in WebSTR searchIndex name mouseOver <b>Repeat motif:</b> $motif ($period bp) <br> <b>Copies in ref:</b> $numCopies <br> <b>Heterozygosity:</b> $het scoreFilter 0 filterByRange.het on filter.het 0:1 filterLimits.het 0:1 detailsScript.histogram.afrHist {"title":"AFR Allele Frequencies","xLabel":"Allele size (repeat copies)"} detailsScript.histogram.amrHist {"title":"AMR Allele Frequencies","xLabel":"Allele size (repeat copies)"} detailsScript.histogram.easHist {"title":"EAS Allele Frequencies","xLabel":"Allele size (repeat copies)"} detailsScript.histogram.eurHist {"title":"EUR Allele Frequencies","xLabel":"Allele size (repeat copies)"} detailsScript.histogram.sasHist {"title":"SAS Allele Frequencies","xLabel":"Allele size (repeat copies)"} track strchive html strchiveNew shortLabel STRchive longLabel STRchive Disease-Associated Short Tandem Repeat Loci type bigBed 9 + itemRgb on bigDataUrl /gbdb/$D/strVar/strchive.bb visibility pack superTrack strVar pack url https://strchive.org/loci/$$ urlLabel STRchive locus page searchIndex name mouseOver <b>Gene:</b> $gene <br> <b>Motif:</b> $referenceMotif <br> <b>Minimum pathogenic repeat:</b> $pathogenicMin <br> <b>Mode of inheritance:</b> $inheritance <br> <b>Evidence:</b> $evidence <br> <b>Associated disease(s):</b> $disease filterValues.evidence Definitive,Strong,Moderate,Limited,Provisional,Disputed,Refuted filterType.evidence multiple filterLabel.evidence Evidence for the locus-disease association # written by the strchive otto job, kent/src/hg/utils/otto/strchive dataVersion /gbdb/$D/strVar/strchive.version.txt track trexplorer shortLabel TRExplorer longLabel TRExplorer V2 Tandem Repeat Catalog type bigBed 9 + itemRgb on bigDataUrl /gbdb/$D/strVar/trexplorer.bb visibility dense superTrack strVar dense urls locusId="https://trexplorer.broadinstitute.org/index.html?#showRs=1&q=$$" urlLabel TRExplorer locus page searchIndex name mouseOver <b>Motif:</b> $referenceMotif ($motifSize bp) <br> <b>Copies in ref:</b> $numRepeats <br> <b>Purity:</b> $repeatPurity <br> <b>Heterozygosity:</b> $het <br> <b>Gene:</b> $geneName ($geneRegion) filterByRange.het on filter.het 0:1 filterLimits.het 0:1 detailsScript.histogram.tenKAlleleHist {"title":"TenK10K Allele Distribution","xLabel":"Allele size (repeat copies)"} detailsScript.histogram.hprcAlleleHist {"title":"HPRC256 Allele Distribution","xLabel":"Allele size (repeat copies)"} track tommoStr shortLabel ToMMo 61k STR longLabel ToMMo 61KJPN Short Tandem Repeat Allele Counts (Expansion Hunter) type bigBed 9 + itemRgb on bigDataUrl /gbdb/$D/strVar/tommoStr.bb visibility dense superTrack strVar dense searchIndex name mouseOver <b>Motif:</b> $motif ($period bp) <br> <b>Ref copies:</b> $numCopies <br> <b>Mean:</b> $mean, <b>Median:</b> $median <br> <b>Heterozygosity:</b> $het scoreFilter 0 filterByRange.het on filter.het 0:1 filterLimits.het 0:1 detailsScript.histogram.alleleHist {"title":"Allele Count Distribution (61K Japanese)","xLabel":"Allele size (repeat copies)"} track viennaVntr shortLabel 1KG Vienna ONT VNTR longLabel 1000 Genomes Vienna ONT VNTR Allele Statistics (VAMOS, 1,019 samples, long-read) type bigBed 9 + itemRgb on bigDataUrl /gbdb/$D/strVar/viennaVntr.bb visibility dense superTrack strVar dense searchIndex name skipEmptyFields on mouseOver <b>Avg motif:</b> $ruLenAvg bp <br> <b>Median repeat units:</b> $medianRus (range: $minRus-$maxRus) <br> <b>Unique alleles:</b> $numUniqueVntrs <br> <b>Heterozygosity:</b> $het scoreFilter 0 filterByRange.het on filter.het 0:1 filterLimits.het 0:1 dataVersion v1.1