65091fe6f6487c23d650a144e947fc1c582d3f40
max
  Tue Apr 21 02:16:16 2026 -0700
abelSv: move under lrSv supertrack as short-read comparison subtrack

Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a
top-level hg38 track to a subtrack of the lrSv supertrack (parallel
to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina
short-read provenance. The same bigBed is now visible on hg38 in
the long-read SV browsing context. Also:

- Clarify abelSv.html variant counts: 738,624 upstream unique SVs
across both callsets, 737,998 after B37->hg38 liftOver (626
unmapped). B38=458,106, B37lift=279,892.
- lrSv.html: fix triple-slash https:/// in the Ebert et al. Science
reference URL.
- bigBed.html: add closing </li> on the extra-fields pipe-separator
bullet and tighten a comma in the same sentence.

refs #36258, refs #37376

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index f51bf6bfca1..808454bdf4b 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -43,30 +43,69 @@
     filterType.insType multipleListOr
     filterLabel.insType Insertion/Deletion Type
     filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA
     filterType.family multipleListOr
     filterLabel.family Transposon Family
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count
     skipEmptyFields on
     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> ($svType) len=$svLength AF=$af AC=$ac/$an callset=$callset MSQ=$msq
+    skipEmptyFields on
+    skipFields mateChrom,matePos
+    filterValues.svType DEL|deletion,DUP|duplication,INV|inversion,MEI|mobile element insertion,BND|breakend/translocation
+    filterType.svType multipleListOr
+    filterLabel.svType SV Type
+    filterValues.callset B38|Native GRCh38 callset (14623 samples),B37lift|Lifted from GRCh37 callset (8417 samples)
+    filterType.callset multipleListOr
+    filterLabel.callset Source Callset
+    filterValues.filter PASS|High confidence,LOW|Low confidence
+    filterType.filter multipleListOr
+    filterLabel.filter Filter Status
+    filterByRange.af on
+    filter.af 0:1
+    filterLimits.af 0:1
+    filterLabel.af Allele Frequency (AF)
+    filterByRange.svLength on
+    filter.svLength 0:250000000
+    filterLimits.svLength -1:250000000
+    filterLabel.svLength SV Length (bp; -1 for BND)
+    filterByRange.msq on
+    filter.msq 0:500
+    filterLimits.msq 0:500
+    filterLabel.msq Mean Sample Quality (MSQ)
+    filterByRange.ac on
+    filter.ac 0:30000
+    filterLimits.ac 0:30000
+    filterLabel.ac Allele Count (AC)
+    url https://www.nature.com/articles/s41586-020-2371-0
+    urlLabel Abel et al, Nature 2020:
+
     track onekg3202Sr
     parent lrSv
     bigDataUrl /gbdb/$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) len=$svLen AF=$alleleFreq AC=$alleleCount/$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