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/sfariSparkExomes.html src/hg/makeDb/trackDb/human/sfariSparkExomes.html
index 606d082e50a..a7a30e0d2d8 100644
--- src/hg/makeDb/trackDb/human/sfariSparkExomes.html
+++ src/hg/makeDb/trackDb/human/sfariSparkExomes.html
@@ -6,31 +6,31 @@
 of 142,357 individuals with whole-exome (WES) and 12,519 with whole-genome sequencing (WGS).
 The data contains 32,559 trios and 8,895 quads (one sibling without autism), and 824 twins.
 </p>
 
 <p>
 The same frequencies shown here are also available publicly on the
 <a href="https://genomes.sfari.org/" target="_blank">SFARI Genome Browser</a>.
 See (SPARK et al, Neuron 2018) for details.
 </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>sfariSparkExomes</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>
 Allele frequencies can also be displayed on the
 <a href="https://genomes.sfari.org/" target="_blank">SFARI Genome Browser</a>.
 Full CRAMs and VCFs with genotypes are available from
 <a href="https://base.sfari.org/" target="_blank">SFARI Base</a>.
 They require a data access request, which is usually reviewed quickly. More information is
 available in the
 <a href="https://cohorts-cdn.simonsfoundation.org/spark/researcher_packets/SPARK_SFARI_Researcher_Welcome_Packet.pdf"
 target="_blank">SPARK Welcome Packet</a>.
 </p>
 
@@ -103,22 +103,22 @@
     contamination (&ge;5%), insufficient coverage (&lt;20x in &lt;80% of
     targets), sex discordance, pedigree/IBD inconsistencies,
     unregistered relationships, unexpected duplicates, or excess
     relatedness, after which QC-passing individuals (selecting the
     most recent passing sample per person) were retained for
     variant calling and joint genotyping.
     </li>
 </ul>
 <p>
 We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track.
 For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>.
 </p>
 
 <h2>References</h2>
 <p>
-SPARK Consortium. Electronic address: pfeliciano@simonsfoundation.org, SPARK Consortium.
+SPARK Consortium. Electronic address: <A HREF="mailto:&#112;f&#101;&#108;&#105;&#99;&#105;&#97;&#110;o&#64;&#115;&#105;&#109;&#111;&#110;&#115;f&#111;&#117;&#110;&#100;a&#116;&#105;&#111;&#110;.&#111;&#114;g">&#112;f&#101;&#108;&#105;&#99;&#105;&#97;&#110;o&#64;&#115;&#105;&#109;&#111;&#110;&#115;f&#111;&#117;&#110;&#100;a&#116;&#105;&#111;&#110;.&#111;&#114;g</A><!-- above address is pfeliciano at simonsfoundation.org -->, SPARK Consortium.
 <a href="https://linkinghub.elsevier.com/retrieve/pii/S0896-6273(18)30018-7" target="_blank">
 SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research</a>.
 <em>Neuron</em>. 2018 Feb 7;97(3):488-493.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29420931" target="_blank">29420931</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7444276/" target="_blank">PMC7444276</a>
 </p>