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/tommo60kjpn.html src/hg/makeDb/trackDb/human/tommo60kjpn.html
index 3c89894d2c9..2907bcf2a59 100644
--- src/hg/makeDb/trackDb/human/tommo60kjpn.html
+++ src/hg/makeDb/trackDb/human/tommo60kjpn.html
@@ -1,50 +1,50 @@
 <h2>Description</h2>
 <p>
 An allele frequency panel based on short-read whole-genome sequencing analysis of 61,000 Japanese
 individuals, produced by the
 <a href="https://jmorp.megabank.tohoku.ac.jp/downloads" target="_blank">Tohoku Medical Megabank
 Organization (ToMMo)</a> at Tohoku University. The project includes other datatypes such as STRs,
 long-read SVs and short-read CNVs.
 </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>tommo60kjpn</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>
 The original data can also be downloaded from the <a href="https://jmorp.megabank.tohoku.ac.jp"
 target="_blank">jMorp website</a>, specifically the
 <a href="https://jmorp.megabank.tohoku.ac.jp/downloads" target="_blank">Downloads</a> section.
 </p>
 
 <h2>Methods</h2>
 <p>
 Genomic DNA was obtained from peripheral blood, saliva, or cord blood samples. Sequencing was
 performed on Illumina HiSeq 2500, HiSeq X Five, NovaSeq 6000, and MGI DNBSeq G400/T7 instruments.
 Reads were aligned to the GRCh38 reference using BWA 0.7.15 or BWA-mem2 2.1. Alignments underwent
 base quality score recalibration (BQSR) with the GATK BaseRecalibrator tool. SNV/indel calling was
 performed using GATK HaplotypeCaller, followed by multisample joint genotyping with Sentieon
 Genomics tools and variant quality score recalibration (VQSR) filtering. Related samples were
 identified and removed using KING 2.3.1, resulting in the final allele frequency panel.
 </p>
 <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>
 Tadaka S, Kawashima J, Hishinuma E, Saito S, Okamura Y, Otsuki A, Kojima K, Komaki S, Aoki Y, Kanno
 T <em>et al</em>.
 <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad978" target="_blank">
 jMorp: Japanese Multi-Omics Reference Panel update report 2023</a>.
 <em>Nucleic Acids Res</em>. 2024 Jan 5;52(D1):D622-D632.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37930845" target="_blank">37930845</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10767895/" target="_blank">PMC10767895</a>
 </p>