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/scripts/lrSv/databases.tsv src/hg/makeDb/scripts/lrSv/databases.tsv
index a0e381c8c43..f793e5f8acf 100644
--- src/hg/makeDb/scripts/lrSv/databases.tsv
+++ src/hg/makeDb/scripts/lrSv/databases.tsv
@@ -4,32 +4,32 @@
 #   label          - human-readable label shown in filter dropdown and detail page
 #   bbPath         - path to the source bigBed file (under /gbdb/hg38/lrSv/)
 #   valueField     - autoSql field name to extract for the per-db value column.
 #                    Special values:
 #                      UNKNOWN  - emit literal "unknown" (db has no real AC)
 #                      SPLIT    - use affField/healField for two output columns
 #   valueLabel     - text shown after the dataset name on the detail page
 #                    (typically "AC", but "samples" for gustafson)
 #   affField       - SPLIT mode: expression for affected AC (supports "a+b")
 #   healField      - SPLIT mode: expression for healthy AC
 #   afField        - autoSql field name(s) to use for max-AF aggregation,
 #                    comma-separated. "" means no AF available.
 # Order here = order of per-db columns in the output bigBed.
 #key	label	bbPath	valueField	valueLabel	affField	healField	afField
 CoLoRSdb	CoLoRSdb 1,427 (PacBio)	/gbdb/hg38/lrSv/colorsDb/sv.hg38.bb	AC	AC			AF
-1000G-ONT-Vienna	1KG ONT Vienna 1,019	/gbdb/hg38/lrSv/1kgOnt.bb	AC	AC			alleleFreq
-1000G-ONT	1KG ONT 100 (Gustafson)	/gbdb/hg38/lrSv/gustafson.bb	sampleCount	samples
+1000G-ONT-Vienna	1KG ONT 1019	/gbdb/hg38/lrSv/1kgOnt.bb	AC	AC			alleleFreq
+1000G-ONT	1KG ONT UW 100	/gbdb/hg38/lrSv/gustafson.bb	sampleCount	samples
 AoU1K	All of Us 1,027 (PacBio)	/gbdb/hg38/lrSv/aou1k.bb	AC	AC			afAfr,afAmr,afEas,afEur,afSas
 Han945	Han Chinese 945	/gbdb/hg38/lrSv/han945.bb	AC	AC			alleleFreq
 TommoJapan	ToMMo 333 (Japanese)	/gbdb/hg38/lrSv/tommoJp.bb	AC	AC			alleleFreq
 GA4K	GA4K 502 (rare disease)	/gbdb/hg38/lrSv/ga4kSv.bb	AC	AC			alleleFreq
 deCODE	deCODE 3,622 (Icelandic)	/gbdb/hg38/lrSv/decodeSv.bb	UNKNOWN	AC
 HPRCv2.1	HPRC v2.1 233	/gbdb/hg38/lrSv/hprc2v21.bb	AC	AC			alleleFreq
 HGSVC2	HGSVC2 32	/gbdb/hg38/lrSv/hgsvc2.bb	AC	AC
 HGSVC3	HGSVC3 65	/gbdb/hg38/lrSv/hgsvc3.bb	AC	AC
 # KimPD (Kim PD Brain 100) is held on dev/alpha until published; it has
 # breakend artifacts up to 190 Mb, so it is excluded from the lrSvAll merge.
 ArabUAE53	Arab APR 53	/gbdb/hg38/lrSv/apr.bb	AC	AC			alleleFreq
 China58	CPC 58 (Chinese)	/gbdb/hg38/lrSv/cpc1.bb	AC	AC			alleleFreq
 Svatalog101	SVatalog 101	/gbdb/hg38/lrSv/chirmade101.bb	UNKNOWN	AC
 CARD	NIH CARD 351 (brain)	/gbdb/hg38/lrSv/card.bb	AC	AC			alleleFreq
-Noyvert888	Noyvert 888 (1000G ONT)	/gbdb/hg38/lrSv/noyvert.bb	AC	AC			AF
+Noyvert888	1KG ONT Boehringer 888	/gbdb/hg38/lrSv/noyvert.bb	AC	AC			AF