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/saudi.html src/hg/makeDb/trackDb/human/saudi.html
index b35cd9993ba..fdb41d9141d 100644
--- src/hg/makeDb/trackDb/human/saudi.html
+++ src/hg/makeDb/trackDb/human/saudi.html
@@ -2,50 +2,50 @@
 <p>
 Variant frequencies from 302 whole genomes at 30x coverage from the
 <a href="https://www.vision2030.gov.sa/en/explore/projects/the-saudi-genome-program"
 target="_blank">Saudi Genome Program</a>. The genotyping data and imputations from 3,352
 individuals do not seem to be available publicly.
 </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>saudi</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 were downloaded from
 <a href="https://figshare.com/articles/dataset/A_list_of_Saudi_Arabian_variants_and_their_allele_frequencies/28059686/1?file=51297884"
 target="_blank">Figshare</a> and converted to VCF.
 </p>
 
 <h2>Methods</h2>
 <p>
 Whole-genome sequencing of 302 Saudi Arabian individuals was performed on the Illumina HiSeq
 X Ten platform using TruSeq Nano DNA library preparation at 30x target coverage. Sequencing and
 initial bioinformatics processing were carried out by deCODE Genetics (Reykjav&iacute;k, Iceland).
 Reads were aligned to the GRCh38 reference genome using BWA 0.7.10. Per-sample variant calling
 was performed with GATK HaplotypeCaller, followed by joint genotyping using CombineGVCFs and
 GenotypeGVCFs. Variant quality score recalibration (VQSR) was applied for both SNPs and indels.
 The final autosomal callset contains 25.5 million variants across the 302 individuals.
 </p>
 <p>
 The variant data were downloaded from
 <a href="https://figshare.com/articles/dataset/A_list_of_Saudi_Arabian_variants_and_their_allele_frequencies/28059686/1?file=51297884"
 target="_blank">Figshare</a> and converted to VCF format using a custom script.
-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>
 Malomane DK, Williams MP, Huber CD, Mangul S, Abedalthagafi M, Chiang CWK.
 <a href="https://doi.org/10.1101/2025.01.10.632500" target="_blank">
 Patterns of population structure and genetic variation within the Saudi Arabian population</a>.
 <em>bioRxiv</em>. 2025 Jan 13;.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39868174" target="_blank">39868174</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761371/" target="_blank">PMC11761371</a>
 </p>