38bafc856320cf5360e0482faeee72b78f2ea963
lrnassar
  Tue May 5 14:13:30 2026 -0700
QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642

Mechanical fixes across 18 per-subtrack description pages:
- Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm).
- Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv.

Added missing References sections:
- allofus.html: All of Us Research Program 2024 Nature.
- topmed.html: Taliun 2021 Nature.
- alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet).
- gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet).
- varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP).

Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub.

All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.

diff --git src/hg/makeDb/trackDb/human/hgdp1kFreq.html src/hg/makeDb/trackDb/human/hgdp1kFreq.html
index 9a200a62463..1dd30adba3d 100644
--- src/hg/makeDb/trackDb/human/hgdp1kFreq.html
+++ src/hg/makeDb/trackDb/human/hgdp1kFreq.html
@@ -9,31 +9,31 @@
 
 <p>
 This track shows allele frequencies only. The full phased genotype data with haplotype
 clustering display is available in the
 <a href="hgTrackUi?g=hgdp1k">gnomAD HGDP+1000G track</a> under Phased Variants.
 The track here does not include the full variant frequencies for all subpopulations, instead, 
 it aggregates frequencies to the main groups, AFR, AMI, AMR, ASJ, EAS, FIN, MID, NFE, OTH, SAS. 
 To access the full frequency information, use the track under "Phased 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">REST API</a> can be used; the
+For programmatic access, our <a href="https://api.genome.ucsc.edu" target="_blank">REST API</a> can be used; the
 track name is <em>hgdp1kFreq</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>
 The original VCFs with full genotypes can also be downloaded from
 <a href="https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg"
 target="_blank">gnomAD Downloads</a>.
 </p>
 
 <h2>Methods</h2>
 <p>
 The gnomAD project reprocessed 4,094 whole genomes from the 1000 Genomes Project and the Human
 Genome Diversity Project (HGDP) through a unified pipeline. Sequencing was performed on Illumina
 platforms at a mean coverage of 32&ndash;34x. Reads were aligned to GRCh38 (hs38DH reference with