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/alfaVcf.html src/hg/makeDb/trackDb/human/alfaVcf.html
index d4949705133..ee9d5f9ce22 100644
--- src/hg/makeDb/trackDb/human/alfaVcf.html
+++ src/hg/makeDb/trackDb/human/alfaVcf.html
@@ -4,41 +4,41 @@
 Aggregator (ALFA)</a> pipeline computes allele frequencies from approved, unrestricted dbGaP studies
 and makes them publicly available through dbSNP. Its goal is to release frequency data from over
 one million dbGaP subjects to aid discoveries involving common and rare variants with biological
 or disease relevance. The R4 release includes 408,709 subjects and allele frequencies for
 15.5 million rs sites, including nearly one million ClinVar variants.
 </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>alfaVcf</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>
 We converted the NCBI track hub to VCF format; the data is freely available.
 Genotype and associated individual-level data are accessible through the dbGaP
 <a href="https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login"
 target="_blank">authorized access request</a> system.
 </p>
 
 <h2>Methods</h2>
 <p>
 The ALFA pipeline processes genotype data from approved, unrestricted dbGaP studies, including
 chip array, exome, and genomic sequencing data. Selected study data undergoes quality assurance
 and transformation to standard VCF format. Variants are converted to SPDI notation and normalized
 using VOCA, then aggregated, remapped, and clustered to existing dbSNP rs identifiers or assigned
 new ones. Sample ancestries are validated using GRAF-pop and assigned to 12 major populations.
 QC exclusions include variants and subjects with call rate &lt;95%, datasets failing Ancestry
 Informative Markers consistency checks, and array datasets with conflicting or flipped allele
 orientation.
 </p>
 <p>
 The ALFA R4 bigBed files (904M variants) were converted to VCF using a custom script, retaining
 the 163M variants with non-zero allele frequency (146M SNPs, 17M indels).
-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>