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/noyvertSv.html src/hg/makeDb/trackDb/human/noyvertSv.html
index 488b8d9039e..e4547b64013 100644
--- src/hg/makeDb/trackDb/human/noyvertSv.html
+++ src/hg/makeDb/trackDb/human/noyvertSv.html
@@ -5,50 +5,44 @@
 Genomes Project, representing five ancestry groups. 
 This dataset and the <a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a> track
 (Schloissnig et al. 2025) are based on the same underlying Oxford Nanopore
 sequencing data; the 888 samples here are a subset of the 1,019 samples in that
 track and only SVs that appear in a single sample (singletons) were removed from this track,
 so this callset is smaller than the Schloissnig dataset. The reason is that
 this callset was created primarily for imputation: The SVs here were merged with
 previously identified short variants from the same individuals to generate a
 multi-ancestry SV imputation reference panel. This panel was used to impute
 SVs in approximately 500,000 UK Biobank participants and test their
 associations with 32 disease-relevant traits.
 </p>
 <p>
 The track contains all 107,445 SVs in the reference panel: 59,953 insertions,
 38,459 deletions, 5,729 inversions, 2,696 breakends, and 608 duplications.
-Variants seen in only a single individual (singletons) were excluded from the
-panel, so every SV shown was observed in at least two individuals; the panel is
-therefore not exhaustive for very rare variants.
 Each variant is annotated with its overall allele frequency; allele
 frequencies across five superpopulations (African, Admixed American, East
 Asian, European, and South Asian); Hardy-Weinberg equilibrium p-values; and
 imputation accuracy metrics from internal leave-one-out validation and UK
 Biobank imputation. For SVs reaching genome-wide significance, the associated
 traits, p-values, and INFO scores are listed on the corresponding variant
 details page.
 </p>
 <p>
-This dataset and the <a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</a> track
-(Schloissnig et al. 2025) are based on the same underlying Oxford Nanopore
-sequencing data; the 888 samples here are a subset of the 1,019 samples in that
-track. The two studies applied different data-processing and SV-calling
-pipelines to address distinct research objectives, so the individual calls are
-only partially concordant. The imputation reference panel, UK Biobank
-imputation results, and SV-wide association study (SV-WAS) results described
-here are specific to this track.
+Although the two studies share the same raw sequencing data, they applied
+different data-processing and SV-calling pipelines to address distinct research
+objectives, so the individual calls are only partially concordant. The
+imputation reference panel, UK Biobank imputation results, and SV-wide
+association study (SV-WAS) results described here are specific to this track.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Items are colored by SV type, matching the other subtracks of the container:
 </p>
 <table class="stdTbl">
   <tr><th style="background-color:#C80000;width:2em">&nbsp;</th>
       <td>Deletion (DEL)</td></tr>
   <tr><th style="background-color:#0000C8;width:2em">&nbsp;</th>
       <td>Insertion (INS)</td></tr>
   <tr><th style="background-color:#00A000;width:2em">&nbsp;</th>
       <td>Duplication (DUP)</td></tr>
   <tr><th style="background-color:#E68C00;width:2em">&nbsp;</th>
       <td>Inversion (INV)</td></tr>