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/hrc.html src/hg/makeDb/trackDb/human/hrc.html
index 1d42232fd08..6a9ac4a0a50 100644
--- src/hg/makeDb/trackDb/human/hrc.html
+++ src/hg/makeDb/trackDb/human/hrc.html
@@ -9,51 +9,51 @@
 <p>
 The contributing studies include the 1000 Genomes Project, UK10K, and many other cohorts.
 Since 1000 Genomes data is already available as a separate track, this track shows only
 the frequencies from the non-1000 Genomes samples (~30,000 individuals), resulting in
 38.3 million variants after lifting from GRCh37 to GRCh38.
 </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>hrc</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 site list file can also be downloaded from the
 <a href="http://www.haplotype-reference-consortium.org/site" target="_blank">HRC website</a>.
-Our Github repo contains a
+Our GitHub repo contains a
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/hrcToVcf.py"
 target="_blank">script</a> that converts the tab-separated file to VCF and lifts it to hg38.
 </p>
 
 <h2>Methods</h2>
 <p>
 The HRC r1.1 site list was downloaded from the
 <a href="http://www.haplotype-reference-consortium.org/site" target="_blank">HRC website</a>
 as a tab-separated file on GRCh37, converted to VCF and lifted to GRCh38 with UCSC liftOver.
 Only frequencies from the non-1000 Genomes samples (~30,000 of the 32,488 total) are included,
 since 1000 Genomes data is available separately. Of 40.4M input variants, 8,052 were unmapped
 by liftOver and 2.1M were present only in 1000 Genomes samples and were dropped, leaving
 38.3M variants.
-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>Credits</h2>
 <p>
 Thanks to the Haplotype Reference Consortium and all contributing studies for making this
 reference panel publicly available.
 </p>
 
 <h2>References</h2>
 <p>
 McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C,
 Danecek P, Sharp K <em>et al</em>.
 <a href="https://doi.org/10.1038/ng.3643" target="_blank">
 A reference panel of 64,976 haplotypes for genotype imputation</a>.
 <em>Nat Genet</em>. 2016 Oct;48(10):1279-83.