90668959b76ef7d792bac3cbc4eb509a58c6c317
chmalee
  Thu Apr 23 11:25:38 2026 -0700
Adding mergeSpannedItems to gnomad CNV and structural variants tracks on hg38, refs Max email

diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.ra src/hg/makeDb/trackDb/human/hg38/gnomad.ra
index 2cad32187f0..97a6eb2c45c 100644
--- src/hg/makeDb/trackDb/human/hg38/gnomad.ra
+++ src/hg/makeDb/trackDb/human/hg38/gnomad.ra
@@ -233,48 +233,50 @@
 filterLabel.af_non_neuro Filter by non-neurological allele frequency
 filter.af_controls 0:1
 filterByRange.af_controls on
 filterLimits.af_controls 0:1
 filterLabel.af_controls Filter by common disease control allele frequency
 filterLabel.svtype Type of Variation
 filterValues.svtype BND|Breakend,CPX|Complex,CTX|Translocation,DEL|Deletion,DUP|Duplication,INS|Insertion,INV|Inversion,MCNV|Multi-allele CNV
 filter.svlen 50:199840172
 filterByRange.svlen on
 filterLabel.svlen Filter by Variant Size
 mouseOverField _mouseOver
 filterValues.FILTER PASS,HIGH_NCR,IGH_MHC_OVERLAP,UNRESOLVED,REFERENCE_ARTIFACT
 filterValuesDefault.FILTER PASS
 filterType.FILTER multipleListAnd
 html gnomadSv.html
+mergeSpannedItems on
 
 
 track gnomadCopyNumberVariants
 parent gnomadVariants on
 bigDataUrl /gbdb/hg38/gnomAD/v4/cnv/gnomad.v4.1.cnv.all.bb
 shortLabel gnomAD Rare CNV Variants
 longLabel Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1
 dataVersion Release 4.1 (November 01, 2023)
 type bigBed 9 +
 itemRgb on
 visibility hide
 url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_cnv_r4
 urlLabel gnomAD Copy number variants Browser
 filterLabel.svtype Type of Variation
 filterValues.svtype DEL|Deletion,DUP|Duplication
 searchIndex name
 mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd}<br> <b>Size of variant</b>: ${svlen}<br> <b>Genes impacted by variant</b>: ${genes}<br> <b>Site frequency (non-neuro control samples)</b>: ${sf}
 html gnomadCNV
+mergeSpannedItems on
 
 track gnomadStr
 parent gnomadVariants on
 shortLabel gnomAD STR
 longLabel Genome Aggregation Database (gnomAD) - Short Tandem Repeat Genotypes at Disease-Associated Loci
 pennantIcon New red ../goldenPath/newsarch.html#041026 "Released Apr. 10, 2026"
 dataVersion gnomAD v3.1.3 STR genotypes (March 2025)
 type bigBed 9 +
 itemRgb on
 bigDataUrl /gbdb/hg38/gnomAD/gnomadStr.bb
 visibility pack
 url https://gnomad.broadinstitute.org/short-tandem-repeat/$$?dataset=gnomad_r3
 urlLabel View at gnomAD
 searchIndex name
 mouseOver <b>Gene:</b> $gene<br> <b>Repeat Motif(s):</b> $motif<br> <b>Number of samples:</b> $nSamples <br> <b>Passing quality filter:</b> $nPass <br> <b>Population sample counts:</b> $populations