0bd565e053abc8c74475f352bedfd37e41312fd2
max
  Wed Aug 12 02:15:40 2026 -0700
lrSv: update noyvertSv docs and align merged-track source labels, refs #37888

Follow-up to author (Boris Noyvert) feedback on the Noyvert/Boehringer
long-read SV dataset.

noyvertSv.html:
- restore neutral wording about the shared 1000G ONT reads; drop the
"independent reprocessing" phrasing and the call-level overlap
interpretation the authors objected to
- note that singletons (SVs in a single sample) were excluded, so the
panel is not exhaustive for the rarest variants
- add the medRxiv preprint link alongside the eLife reference

Give each dataset one consistent name across its subtrack and the merged
(lrSvAll) source filter (databases.tsv + lrSvAll.ra + lrSv.ra):
Noyvert 888 (1000G ONT) -> 1KG ONT Boehringer 888
1KG ONT Vienna 1,019    -> 1KG ONT 1019
1KG ONT 100 (Gustafson) -> 1KG ONT UW 100
The gustafsonSv subtrack short/long labels read 97 samples; the paper and
our track docs report 100 (Gustafson et al. 2024, PMID 39358015), so those
are corrected to 100 as well.
Rebuilt lrSvAll.bb with lrSvMergeAll.py; item count unchanged (2,582,278).

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index ef296a0dc36..b19c31b037b 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -81,32 +81,32 @@
     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 gustafsonSv
     parent longReadVariants
     bigDataUrl /gbdb/$D/lrSv/gustafson.bb
-    shortLabel 1KG ONT UW 97 SVs
-    longLabel Structural Variants from 1000 Genomes University of Washington ONT - 97 samples (Gustafson et al. 2024)
+    shortLabel 1KG ONT UW 100 SVs
+    longLabel Structural Variants from 1000 Genomes University of Washington ONT - 100 samples (Gustafson et al. 2024)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC<br><b>Samples</b>: $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
     filter.insLen 0:25094
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:200
     filterByRange.AC on