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 $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/allofus.html src/hg/makeDb/trackDb/human/allofus.html index 5423ddf05c6..2f26452855d 100644 --- src/hg/makeDb/trackDb/human/allofus.html +++ src/hg/makeDb/trackDb/human/allofus.html @@ -15,49 +15,49 @@ Frequencies are provided both overall and broken down by genetic ancestry using local ancestry inference: European (EUR), East Asian (EAS), African (AFR), Indigenous American (AMR), Oceanian (OCE), and South Asian (SAS). Some variants are flagged with an "NW" tag (not in window) when the variant was not within a genomic window covered by the ancestry reference files; in these cases the closest available position was used for ancestry assignment. </p> <h2>Data Access</h2> <p> The data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, our <a href="https://api.genome.ucsc.edu">REST API</a> can be used; the track name is <em>allofus</em>. For bulk download, the VCF file can be obtained from -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$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> Variant data and individual-level data are accessible through the <a href="https://workbench.researchallofus.org/" target="_blank">All of Us Researcher Workbench</a>, which requires registration and completion of a training program. Aggregate allele frequency data is freely available. </p> <h2>Methods</h2> <p> Whole-genome sequencing was performed on the Illumina NovaSeq 6000 platform with PCR-free library preparation targeting 30x coverage. Reads were aligned to GRCh38 and variants were called using the Illumina DRAGEN (Dynamic Read Analysis for GENomics) pipeline, which performs mapping, alignment, sorting, duplicate marking, and variant calling (SNVs and indels) in a single hardware-accelerated workflow. Joint genotyping was performed across all samples. Quality control included sample-level filtering for contamination, sex discordance, and relatedness, and variant-level filtering using VQSR. Population-specific allele frequencies were determined using local ancestry inference at UCSC by the Ioannidis group. The ancestry breakdown into European, East Asian, African, Indigenous American, Oceanian, and South Asian components is part of a pending publication. </p> <p> -At UCSC, 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>. +At UCSC, 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> The All of Us Research Program is supported by the National Institutes of Health. We thank the participants and the program for making frequency data available. The local ancestry inference was performed by Qudsi Aljabiri and Cole Shanks under Prof. Alexander Ioannidis, UC Santa Cruz. </p>