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/lrSvAll.ra src/hg/makeDb/trackDb/human/lrSvAll.ra
index c07bbf83beb..8c4e3e6627d 100644
--- src/hg/makeDb/trackDb/human/lrSvAll.ra
+++ src/hg/makeDb/trackDb/human/lrSvAll.ra
@@ -1,40 +1,40 @@
 # AUTO-GENERATED by ~/kent/src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
 # Do not edit by hand - re-run the merge script and re-commit.
 
     track lrSvAll
     parent longReadVariants
     bigDataUrl /gbdb/$D/lrSv/lrSvAll.bb
     shortLabel All LR SVs merged
     longLabel All long-read SVs merged across subtracks by exact position, with per-database AC
     type bigBed 9 +
     itemRgb on
     visibility pack
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Sources</b>: $sources<br><b>AF range</b>: $minAF-$maxAF<br><b>AC</b>: $AC
-    filterValues.sources CoLoRSdb|CoLoRSdb 1427 (PacBio),1000G-ONT-Vienna|1KG ONT Vienna 1019,1000G-ONT|1KG ONT 100 (Gustafson),AoU1K|All of Us 1027 (PacBio),Han945|Han Chinese 945,TommoJapan|ToMMo 333 (Japanese),GA4K|GA4K 502 (rare disease),deCODE|deCODE 3622 (Icelandic),HPRCv2.1|HPRC v2.1 233,HGSVC2|HGSVC2 32,HGSVC3|HGSVC3 65,ArabUAE53|Arab APR 53,China58|CPC 58 (Chinese),Svatalog101|SVatalog 101,CARD|NIH CARD 351 (brain),Noyvert888|Noyvert 888 (1000G ONT)
+    filterValues.sources CoLoRSdb|CoLoRSdb 1427 (PacBio),1000G-ONT-Vienna|1KG ONT 1019,1000G-ONT|1KG ONT UW 100,AoU1K|All of Us 1027 (PacBio),Han945|Han Chinese 945,TommoJapan|ToMMo 333 (Japanese),GA4K|GA4K 502 (rare disease),deCODE|deCODE 3622 (Icelandic),HPRCv2.1|HPRC v2.1 233,HGSVC2|HGSVC2 32,HGSVC3|HGSVC3 65,ArabUAE53|Arab APR 53,China58|CPC 58 (Chinese),Svatalog101|SVatalog 101,CARD|NIH CARD 351 (brain),Noyvert888|1KG ONT Boehringer 888
     filterType.sources multipleListOr
     filterLabel.sources Source Database
     filterValues.svType DEL,INS,DUP,INV,CPX,MIXED,INSDEL,TRA,BND
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:30000000
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:600000
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.maxAF 0:1
     filterByRange.maxAF on
     filterLimits.maxAF 0:1
     filterLabel.maxAF Max Allele Frequency (across DBs)
     filter.minAF 0:1
     filterByRange.minAF on
     filterLimits.minAF 0:1
     filterLabel.minAF Min Allele Frequency (across DBs)
     filter.AC 0:30000
     filterByRange.AC on
     filterLabel.AC Total AC (across DBs)
     filter.sourceCount 1:16
     filterByRange.sourceCount on
     filterLabel.sourceCount Number of Source Databases
     skipEmptyFields on
     priority 0