aa61ebc800429515f9ced7e28f669c6042219f43
max
  Wed Mar 18 09:09:13 2026 -0700
varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642

Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and
Methods sections for all 20+ subtrack HTML files with consistent formatting,
sequencing methods from source papers, and links to makeDoc and Github scripts.
Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and
update makeDoc paths accordingly.

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
new file mode 100644
index 00000000000..1d42232fd08
--- /dev/null
+++ src/hg/makeDb/trackDb/human/hrc.html
@@ -0,0 +1,62 @@
+<h2>Description</h2>
+<p>
+The <a href="http://www.haplotype-reference-consortium.org/"
+target="_blank">Haplotype Reference Consortium (HRC)</a> is a collaboration among several
+large sequencing projects to create a reference panel for genotype imputation.
+Release 1.1 contains 64,976 haplotypes from 32,488 whole-genome sequenced samples at
+low coverage (average 7x), with 40 million variant sites (minimum allele count of 5).
+</p>
+<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>.
+</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
+<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>.
+</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.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27548312" target="_blank">27548312</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388176/" target="_blank">PMC5388176</a>
+</p>