38bafc856320cf5360e0482faeee72b78f2ea963 lrnassar Tue May 5 14:13:30 2026 -0700 QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set. diff --git src/hg/makeDb/trackDb/human/varFreqsAll.html src/hg/makeDb/trackDb/human/varFreqsAll.html index d1203549bd7..75b48c59f13 100644 --- src/hg/makeDb/trackDb/human/varFreqsAll.html +++ src/hg/makeDb/trackDb/human/varFreqsAll.html @@ -132,24 +132,67 @@ <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs/populations.tsv" target="_blank">populations.tsv</a>) to make future updates easy. </p> <p> 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. Scripts are available from <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs" target="_blank">Github</a>. </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" target="_blank">REST API</a> +can be used; the track name is <em>varFreqsAll</em>. +</p> +<p> +Because the merged callset includes data from multiple sources whose redistribution +licenses differ, the combined bigBed is <b>not available for download</b> from our +download server. The combined track can be reconstructed from the individual source VCFs +using the +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/varFreqs" +target="_blank">conversion scripts on GitHub</a> together with the +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" +target="_blank">build documentation</a>. Where individual source data is downloadable from UCSC, +the per-subtrack description page indicates the path on our download server. +</p> + <h2>Credits</h2> <p> This track is only possible thanks to the data from millions of volunteers around the world, who donated blood, signed consent forms and provided health information about themselves and sometimes their families. Click on any of the individual tracks in the <a href="hgTrackUi?g=varFreqs">Variant Frequencies</a> supertrack to see the specific credits for each project. Thanks to Alex Ioannidis, UCSC, for the motivation for this track and to Andreas Lahner, MGZ, for feedback. </p> + +<h2>References</h2> +<p> +For primary citations of each source dataset, see the References section on the +<a href="hgTrackUi?g=varFreqs">Variant Frequencies</a> supertrack page. The merged-track +build itself uses the following tools: +</p> +<p> +Danecek P, McCarthy SA. +<a href="https://doi.org/10.1093/bioinformatics/btx100" target="_blank"> +BCFtools/csq: haplotype-aware variant consequences</a>. +<em>Bioinformatics</em>. 2017 Jul 1;33(13):2037-2039. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28205675" target="_blank">28205675</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870570/" target="_blank">PMC5870570</a> +</p> +<p> +McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. +<a href="https://doi.org/10.1186/s13059-016-0974-4" target="_blank"> +The Ensembl Variant Effect Predictor</a>. +<em>Genome Biol</em>. 2016 Jun 6;17(1):122. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27268795" target="_blank">27268795</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893825/" target="_blank">PMC4893825</a> +</p>