cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47
max
  Wed Jul 22 18:09:16 2026 -0700
lrSv cardSv: switch CARD count fields from carrier counts to allele counts

The NIH CARD provider republished the display bigBed with the count columns
changed to diploid allele counts (alleleCount = nabecAlleleCount +
hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC /
nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to
allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted
there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll
carries CARD's allele counts. refs #36258

diff --git src/hg/makeDb/trackDb/human/cardSv.html src/hg/makeDb/trackDb/human/cardSv.html
index 233ee84f1b0..f479b84cf8e 100644
--- src/hg/makeDb/trackDb/human/cardSv.html
+++ src/hg/makeDb/trackDb/human/cardSv.html
@@ -3,53 +3,54 @@
 This track shows structural variants (SVs) identified by Oxford Nanopore
 long-read sequencing of post-mortem brain tissue (prefrontal cortex) from
 351 individuals, generated by the NIH Center for Alzheimer's and Related
 Dementias (NIH CARD) Long-Read Initiative. Structural variants are genomic
 rearrangements larger than about 50 bp, such as deletions, insertions,
 inversions and duplications; because they alter or move large stretches of
 DNA at once they can have outsized effects on gene dosage, gene regulation
 and DNA methylation compared with single-nucleotide changes.
 </p>
 <p>
 The cohort combines two studies: 205 samples of European ancestry from the
 North American Brain Expression Consortium (NABEC, dbGaP phs001300) and 146
 samples of African and African-admixed ancestry from the NIMH Human Brain
 Collection Core (HBCC, dbGaP phs000979). The track contains more than 228,000 SVs called
 against GRCh38: about 127,000 insertions, 102,000 deletions, 431 inversions
-and one tandem duplication. Each record carries the number of carrier samples
-overall and split by cohort (NABEC and HBCC), together with the allele frequency reported
-by the source project.
+and one tandem duplication. Each record carries the alternate allele count
+overall and split by cohort (NABEC and HBCC), together with the allele frequency
+reported by the source project. None of these samples are Alzheimer's disease
+cases; the cohorts are population brain-tissue collections.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Items are colored by SV type, matching the other subtracks of the container:
 <ul>
 <li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li>
 <li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li>
 <li><span style="color: rgb(0,160,0);">Duplications (DUP)</span> - green</li>
 <li><span style="color: rgb(230,140,0);">Inversions (INV)</span> - orange</li>
 </ul>
 </p>
 <p>
 Insertions are placed at the insertion site with a width of 1 bp, and the
 length of the inserted sequence is shown as the insertion length; deletions,
 inversions and the duplication span the affected reference interval. The
 mouseover shows the variant name, SV type, reference and insertion lengths,
-allele frequency and the number of carrier samples split into the NABEC and
+allele frequency and the alternate allele count split into the NABEC and
 HBCC cohorts. Filters are available for SV type, SV length, insertion length,
-carrier count, allele frequency, and the number of carriers in each cohort.
+allele count, allele frequency, and the allele count in each cohort.
 </p>
 
 <h2>Methods</h2>
 <p>
 NABEC samples were sequenced on Oxford Nanopore R9.4.1 and HBCC samples on
 R10.4.1 PromethION flow cells, with a median read N50 of 27 kb and about 40x
 average genome coverage. Structural variants were called both from read
 alignments (minimap2 alignments processed with Sniffles2 v2.3) and from
 de novo assemblies (Shasta v0.11.1 assemblies phased with HapDup v0.12 and
 compared to the reference with Hapdiff). Assembly-based calls were merged
 across samples with Truvari, read-based calls were merged across samples with
 Sniffles2, and the read and assembly sets were then merged together and across
 the two cohorts with Truvari. All processing used the Nanopore Analysis
 Pipeline (NAPU) workflows on the AnVIL/Terra platform; see Kolmogorov et al.
 2023 and Billingsley et al. 2024 for details.