c16022c991b55ffe9bb620746a6101346c920a67
lrnassar
  Tue May 5 14:23:44 2026 -0700
QA: claim cross-checks on varFreqs description pages; correct 1 internal contradiction and update 3 supertrack references to current/canonical papers. refs #36642

alfaVcf.html: the Description claimed "15.5 million rs sites" while the Methods (and the actual VCF, 163,487,286 records) reflected the post-conversion content. Updated the Description to "163 million variants (146 million SNPs and 17 million indels)" so Description and Methods now agree, and removed the outdated ClinVar count.

varFreqs.html (supertrack References):
- ABraOM: replaced Naslavsky 2017 Hum Mutat (the 609-individual exome paper) with Naslavsky 2022 Nat Commun (the 1,171-WGS paper), which is the flagship for the data we actually serve and is what abraom.html cites.
- Mexico Biobank: added Sohail 2023 Nature ("Mexican Biobank advances population and medical genomics of diverse ancestries"), which is the descriptor paper for the 6,011-individual MEGA-array dataset; the supertrack page previously had no MexBB citation.
- ToMMo: replaced Tadaka 2021 NAR (jMorp updates in 2020) with Tadaka 2024 NAR (jMorp Multi-Omics Reference Panel update report 2023), the more recent jMorp release note that tommo60kjpn.html already cites.

Other claims spot-checked against the VCF and verified consistent: TopMed (header NS=150,899 matches the page; 868,581,653 records matches exactly), GenomeAsia (~65M / actual 66.2M; 1,739 individuals from 219 populations confirmed), GA4K (552 samples / AN=1,104 / 36.2M variants all verified), SVatalog (8.8M / actual 8,814,835), Tishkoff (33.6M / actual 33,600,472), Saudi (302 individuals / 25.5M variants).

diff --git src/hg/makeDb/trackDb/human/alfaVcf.html src/hg/makeDb/trackDb/human/alfaVcf.html
index e24d60d4069..a7dea386bf3 100644
--- src/hg/makeDb/trackDb/human/alfaVcf.html
+++ src/hg/makeDb/trackDb/human/alfaVcf.html
@@ -1,23 +1,25 @@
 <h2>Description</h2>
 <p>
 The <a href="https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/" target="_blank">NCBI ALlele Frequency
 Aggregator (ALFA)</a> pipeline computes allele frequencies from approved, unrestricted dbGaP studies
 and makes them publicly available through dbSNP. Its goal is to release frequency data from over
 one million dbGaP subjects to aid discoveries involving common and rare variants with biological
-or disease relevance. The R4 release includes 408,709 subjects and allele frequencies for
-15.5 million rs sites, including nearly one million ClinVar variants.
+or disease relevance. The R4 release aggregates allele frequencies from 408,709 subjects.
+After conversion to VCF and removal of zero-frequency entries, the UCSC track contains
+163 million variants (146 million SNPs and 17 million indels), including hundreds of
+thousands of ClinVar variants.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The data can be explored interactively with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the
 <a href="../cgi-bin/hgIntegrator">Data Integrator</a>.
 For programmatic access, our <a href="https://api.genome.ucsc.edu" target="_blank">REST API</a> can be used; the
 track name is <em>alfaVcf</em>.
 For bulk download, the VCF file can be obtained from
 <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/" target="_blank">our download server</a>.
 </p>
 <p>
 We converted the NCBI track hub to VCF format; the data is freely available.
 Genotype and associated individual-level data are accessible through the dbGaP