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/srSv.ra src/hg/makeDb/trackDb/human/srSv.ra
new file mode 100644
index 00000000000..31780b2f3b1
--- /dev/null
+++ src/hg/makeDb/trackDb/human/srSv.ra
@@ -0,0 +1,137 @@
+track srSv
+superTrack on
+shortLabel Short-read SVs
+longLabel Structural Variants from Short-read Sequencing (comparators for the long-read SV supertrack)
+group varRep
+visibility hide
+# Supertrack-level filters, mirroring the lrSv structure so users moving
+# between long- and short-read SV tracks get the same UI. Cart values
+# stored under "srSv.filter.<field>.min/max" are inherited by every
+# subtrack via cartOptionalStringClosestToHome() walking tdb->parent.
+filterValues.svType DEL,INS,INV,CPX,DUP,CNV,CTX,INSDEL,MIXED,BND,MEI,TRA
+filterType.svType multipleListOr
+filterLabel.svType SV Type
+filter.svLen 0:250000000
+filterByRange.svLen on
+filterLabel.svLen SV Length (bp)
+filter.insLen 0:1000000
+filterByRange.insLen on
+filterLabel.insLen Insertion Length (bp)
+filter.AC 0:30000
+filterByRange.AC on
+filterLabel.AC Allele Count
+noScoreFilter on
+
+    track abelSv
+    parent srSv
+    bigDataUrl /gbdb/$D/srSv/abelSv.bb
+    shortLabel CCDG 17795 SR SVs
+    longLabel Structural Variants from 17,795 Genomes - Illumina SHORT-READ CCDG callset (Abel et al. 2020)
+    type bigBed 9 +
+    itemRgb on
+    visibility dense
+    mouseOver <b>$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 srSv
+    bigDataUrl /gbdb/$D/srSv/onekg3202sr.bb
+    shortLabel 1KG 3202 SR SVs
+    longLabel 1000 Genomes 3202-sample Illumina SHORT-READ GATK-SV callset (Byrska-Bishop 2022)
+    type bigBed 9 +
+    itemRgb on
+    visibility dense
+    mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber popMax=$popmaxAf
+    filterValues.svType DEL,INS,DUP,INV,CPX,CTX,CNV
+    filterType.svType multipleListOr
+    filterLabel.svType SV Type
+    filter.svLen 0:154807729
+    filterByRange.svLen on
+    filterLabel.svLen SV Length
+    filter.insLen 0:178243
+    filterByRange.insLen on
+    filterLabel.insLen Insertion Length
+    filter.AC 0:6404
+    filterByRange.AC on
+    filterLabel.AC Allele Count
+    filter.alleleFreq 0:1
+    filterByRange.alleleFreq on
+    filterLimits.alleleFreq 0:1
+    filterLabel.alleleFreq Allele Frequency (all)
+    filter.popmaxAf 0:1
+    filterByRange.popmaxAf on
+    filterLimits.popmaxAf 0:1
+    filterLabel.popmaxAf Population Max AF
+    filter.afAfr 0:1
+    filterByRange.afAfr on
+    filterLimits.afAfr 0:1
+    filterLabel.afAfr AF African
+    filter.afEur 0:1
+    filterByRange.afEur on
+    filterLimits.afEur 0:1
+    filterLabel.afEur AF European
+    skipEmptyFields on
+
+    track tommoJpCnv
+    parent srSv
+    container multiWig
+    aggregate transparentOverlay
+    showSubtrackColorOnUi on
+    shortLabel ToMMo 48K CNV SR
+    longLabel CNV Carrier Counts from 48,874 Japanese Individuals (ToMMo 48KJPN-CNV, short-read WGS; 1 kb bins)
+    type bigWig 0 48874
+    autoScale on
+    viewLimits 0:1000
+    viewLimitsMax 0:48874
+    maxHeightPixels 100:32:8
+    visibility full
+    priority 2.5
+
+        track tommoJpCnvLoss
+        parent tommoJpCnv
+        bigDataUrl /gbdb/$D/srSv/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/srSv/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