383da828477aad2b3c6053880a64fdbfc2a00cd9
max
  Thu Mar 19 02:30:41 2026 -0700
Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642

Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese"
to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland"
to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar,
quote all target=_blank attributes, capitalize GitHub consistently, and
fix bioRxiv citation formatting in trexplorer.html.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/sfariSparkExomes.html src/hg/makeDb/trackDb/human/sfariSparkExomes.html
index e32c9ace340..606d082e50a 100644
--- src/hg/makeDb/trackDb/human/sfariSparkExomes.html
+++ src/hg/makeDb/trackDb/human/sfariSparkExomes.html
@@ -9,31 +9,31 @@
 
 <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
 track name is <em>sfariSparkExomes</em>.
 For bulk download, the VCF file can be obtained from
-<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/varFreqs/" target="_blank">our download server</a>.
+<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>
 
 <h2>Methods</h2>
 
 <p>The genome browser track project was approved by the Simons Foundation under request
@@ -97,28 +97,28 @@
     (CHIP). SFARI performed SNV/indel calling via DeepVariant and
     GATK to generate gVCFs, pairwise relatedness inferred using
     PLINK v1.9 IBD estimates from common SNPs (AF &ge; 0.01, dbSNP
     v151) with &ge;15% relatedness flagged, and comprehensive
     individual- and family-level quality control executed using the
     internal GenomeCheckMate pipeline to exclude samples based on
     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>.
+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.
 <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>