f058c8fe4601b223ff47468eb3525c05ccd03850
max
  Wed Apr 22 09:17:17 2026 -0700
srSv: new short-read SV supertrack, split out of lrSv

Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr,
tommoJpCnv) out of the Long-read SV supertrack into a new sibling
supertrack srSv (Short-read SVs), so the lrSv collection contains
only long-read callsets. Filter fields (svType, svLen, insLen, AC)
are mirrored at the srSv supertrack level to keep the UX parallel
to lrSv.

- trackDb: new human/srSv.ra with the three subtrack stanzas and
updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas
removed from human/lrSv.ra. human/trackDb.ra now includes
srSv.ra. Also a new human/srSv.html overview page; the SR rows
and SR-specific paragraphs removed from human/lrSv.html.
- Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/
{lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to
scripts/srSv/ with git mv (history preserved) and renamed to
drop the "lrSv" prefix. Internal path references in abelSvBuild.sh
and abelSvVcfToBed.py updated.
- makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and
extended with the onekg3202Sr and tommoJpCnv sections moved from
lrSv.txt. lrSv.txt leaves a pointer.
- Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr,
lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*.
/gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and
/gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/.

refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 2f553ecbf1e..777dc5bd0bd 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -75,111 +75,30 @@
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:48091
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.AC 0:1816
     filterByRange.AC on
     filterLabel.AC Allele Count
     skipEmptyFields on
     dataVersion 1.1
     priority 2
 
-    track abelSv
-    parent lrSv
-    bigDataUrl /gbdb/$D/abelSv/abelSv.bb
-    shortLabel CCDG 17795 SR SVs
-    longLabel Structural Variants from 17,795 Genomes - Illumina SHORT-READ CCDG callset (Abel et al. 2020) - included for comparison
-    type bigBed 9 +
-    itemRgb on
-    visibility dense
-    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$af AC=$AC/$an callset=$callset MSQ=$msq
-    skipEmptyFields on
-    skipFields mateChrom,matePos
-    filterValues.svType DEL|deletion,DUP|duplication,INV|inversion,MEI|mobile element insertion,BND|breakend/translocation
-    filterType.svType multipleListOr
-    filterLabel.svType SV Type
-    filterValues.callset B38|Native GRCh38 callset (14623 samples),B37lift|Lifted from GRCh37 callset (8417 samples)
-    filterType.callset multipleListOr
-    filterLabel.callset Source Callset
-    filterValues.filter PASS|High confidence,LOW|Low confidence
-    filterType.filter multipleListOr
-    filterLabel.filter Filter Status
-    filterByRange.af on
-    filter.af 0:1
-    filterLimits.af 0:1
-    filterLabel.af Allele Frequency (AF)
-    filterByRange.svLen on
-    filter.svLen 0:250000000
-    filterLimits.svLen -1:250000000
-    filterLabel.svLen SV Length (bp; -1 for BND)
-    filter.insLen 0:8545
-    filterByRange.insLen on
-    filterLabel.insLen Insertion Length
-    filterByRange.msq on
-    filter.msq 0:500
-    filterLimits.msq 0:500
-    filterLabel.msq Mean Sample Quality (MSQ)
-    filterByRange.AC on
-    filter.AC 0:30000
-    filterLimits.AC 0:30000
-    filterLabel.AC Allele Count (AC)
-    url https://www.nature.com/articles/s41586-020-2371-0
-    urlLabel Abel et al, Nature 2020:
-
-    track onekg3202Sr
-    parent lrSv
-    bigDataUrl /gbdb/$D/lrSv/onekg3202sr.bb
-    shortLabel 1KG 3202 SR SVs
-    longLabel 1000 Genomes 3202-sample Illumina SHORT-READ GATK-SV callset (Byrska-Bishop 2022) - included for comparison
-    type bigBed 9 +
-    itemRgb on
-    visibility dense
-    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber popMax=$popmaxAf
-    filterValues.svType DEL,INS,DUP,INV,CPX,CTX,CNV
-    filterType.svType multipleListOr
-    filterLabel.svType SV Type
-    filter.svLen 0:154807729
-    filterByRange.svLen on
-    filterLabel.svLen SV Length
-    filter.insLen 0:178243
-    filterByRange.insLen on
-    filterLabel.insLen Insertion Length
-    filter.AC 0:6404
-    filterByRange.AC on
-    filterLabel.AC Allele Count
-    filter.alleleFreq 0:1
-    filterByRange.alleleFreq on
-    filterLimits.alleleFreq 0:1
-    filterLabel.alleleFreq Allele Frequency (all)
-    filter.popmaxAf 0:1
-    filterByRange.popmaxAf on
-    filterLimits.popmaxAf 0:1
-    filterLabel.popmaxAf Population Max AF
-    filter.afAfr 0:1
-    filterByRange.afAfr on
-    filterLimits.afAfr 0:1
-    filterLabel.afAfr AF African
-    filter.afEur 0:1
-    filterByRange.afEur on
-    filterLimits.afEur 0:1
-    filterLabel.afEur AF European
-    skipEmptyFields on
-
     track gustafsonSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/gustafson.bb
     shortLabel 1KG ONT 100 SVs
     longLabel Structural Variants from 100 1000 Genomes ONT Samples (Gustafson et al. 2024)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC samples=$sampleCount
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:98289
     filterByRange.svLen on
     filterLabel.svLen SV Length
@@ -246,63 +165,30 @@
     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
     skipEmptyFields on
     urls chr2="hgTracks?position=$$"
 
-    track tommoJpCnv
-    parent lrSv
-    container multiWig
-    aggregate transparentOverlay
-    showSubtrackColorOnUi on
-    shortLabel ToMMo 48K CNV SR
-    longLabel CNV Carrier Counts from 48,874 Japanese Individuals (ToMMo 48KJPN-CNV, short-read WGS; 1 kb bins) - included for comparison
-    type bigWig 0 48874
-    autoScale on
-    viewLimits 0:1000
-    viewLimitsMax 0:48874
-    maxHeightPixels 100:32:8
-    visibility full
-    priority 2.5
-
-        track tommoJpCnvLoss
-        parent tommoJpCnv
-        bigDataUrl /gbdb/$D/lrSv/tommoJpCnvLoss.bw
-        shortLabel ToMMo CNV Loss
-        longLabel Samples with copy-number loss (CN<2) per 1 kb bin, ToMMo 48KJPN-CNV
-        type bigWig 0 48874
-        color 200,0,0
-        altColor 200,0,0
-
-        track tommoJpCnvGain
-        parent tommoJpCnv
-        bigDataUrl /gbdb/$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/$D/lrSv/tommoJp.bb
     shortLabel ToMMo 333 SVs
     longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$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