2e0addd016cfcbf61485b90d8980a8d75be622c2
lrnassar
Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258
After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv 133,886 -> 119,453 displayed
gustafsonSv 113,696 -> 113,159 displayed
chirmade101 87,183 -> 87,068 displayed
aou1k 541,049 -> 540,155 displayed
hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).
diff --git src/hg/makeDb/trackDb/human/decodeSv.html src/hg/makeDb/trackDb/human/decodeSv.html
index e5940527f8c..21dddbcebb1 100644
--- src/hg/makeDb/trackDb/human/decodeSv.html
+++ src/hg/makeDb/trackDb/human/decodeSv.html
@@ -35,32 +35,33 @@
page also shows the coordinates of that region (TRRBEGIN / TRREND from the
source VCF), which can be useful context for repeat-mediated insertions and
deletions.
Methods
Beyter et al. 2021 performed Oxford Nanopore long-read sequencing of 3,622
Icelanders recruited through deCODE genetics and detected a median of
22,636 SVs per individual (13,353 insertions and 9,474 deletions). Across
the cohort they derived a set of 133,886 reliably genotyped SV alleles,
imputed those alleles into 166,281 chip-typed Icelanders, and tested them
for association with disease and quantitative traits (notably including a
rare PCSK9 deletion associated with lower LDL-cholesterol and a
multi-allelic 57-bp VNTR in ACAN associated with adult height). The
-track shown here displays the 133,886 high-confidence SV sites: 55,649
-deletions, 75,050 insertions and 3,187 combined insertion/deletion events.
+track shown here displays 119,453 unique high-confidence SV sites (exact-duplicate
+records present in the release have been collapsed): 41,216 deletions, 75,050
+insertions and 3,187 combined insertion/deletion events.
The release is site-only (no per-sample genotypes or allele frequencies),
so the track cannot be filtered by AF/AC.
The VCF ont_sv_high_confidence_SVs.sorted.vcf.gz was downloaded
from the deCODE genetics
LRS_SV_sets GitHub repository.
The step-by-step build commands (download, format conversion, bigBed build)
are recorded in the UCSC makeDoc for this track container:
doc/hg38/lrSv.txt. The conversion scripts and autoSql schemas live in