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/sgdpFreq.html src/hg/makeDb/trackDb/human/sgdpFreq.html
index adecc0755b3..fbaa4472bf3 100644
--- src/hg/makeDb/trackDb/human/sgdpFreq.html
+++ src/hg/makeDb/trackDb/human/sgdpFreq.html
@@ -14,53 +14,53 @@
 This track shows allele frequencies only. The full phased genotype data with haplotype
 clustering display is available in the
 <a href="hgTrackUi?g=sgdp">SGDP track</a> under Phased Variants.
 Not all SGDP data is public, so this track contains only 279 genomes.
 The hg38 data was lifted from hg19.
 </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>sgdpFreq</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 source VCFs are available from
 <a href="https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/"
 target="_blank">https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/</a>.
 </p>
 
 <h2>Methods</h2>
 <p>
 High-coverage whole-genome sequencing of 300 individuals (279 publicly available) from 142
 diverse populations was performed on Illumina instruments using PCR-free library preparation at
 an average depth of 43x. Reads were aligned to the hs37d5 reference (GRCh37 with decoy
 sequences) using BWA-MEM 0.7.12. SNP and indel genotyping was performed using GATK
 HaplotypeCaller with joint genotyping across all samples. An independent indel callset was
 generated using FermiKit for improved sensitivity at complex variants. The final dataset
 contains 34.4 million SNPs and 2.1 million short indels.
 </p>
 <p>
 The VCFs were merged with bcftools and lifted to hg38 with CrossMap. At UCSC, genotypes were
 stripped to produce a sites-only frequency VCF retaining the existing AC, AF, and AN INFO fields.
-We provide documentation that indicates how all source files 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.
-Python scripts 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 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.
+Python scripts 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>
 This project was funded by the Simons Foundation. Thanks to David Reich and Swapan
 Mallick for help with importing the data.
 </p>
 
 <h2>References</h2>
 <p>
 Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S,
 Tandon A <em>et al</em>.
 <a href="https://doi.org/10.1038/nature18964" target="_blank">
 The Simons Genome Diversity Project: 300 genomes from 142 diverse populations</a>.
 <em>Nature</em>. 2016 Oct 13;538(7624):201-206.