99ae46aca64e768875e6cbb2a232a0648bea5344 max Fri May 15 10:13:21 2026 -0700 varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/allofus.html src/hg/makeDb/trackDb/human/allofus.html index 13901cc87c6..8ea4960da35 100644 --- src/hg/makeDb/trackDb/human/allofus.html +++ src/hg/makeDb/trackDb/human/allofus.html @@ -1,73 +1,69 @@ <h2>Description</h2> <p> The <a href="https://allofus.nih.gov/" target="_blank">All of Us</a> Research Program is a large-scale biomedical research initiative launched by the U.S. National Institutes of Health (NIH) in 2018. Its goal is to build one of the most diverse health databases, enrolling over one million participants who reflect the full diversity of the United States, including groups that have been historically underrepresented in biomedical research. Participants contribute health surveys, electronic health records (EHR), physical measurements, and biosamples for genomic analysis. </p> <p> This track shows allele frequencies from the v7 short-read whole-genome sequencing (srWGS) release of 245,388 participants. A minimum allele count filter of ≥20 was applied. 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" target="_blank">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/hg38/varFreqs/" target="_blank">our download server</a>. +Due to license restrictions, the data for this track cannot be downloaded from the UCSC +Genome Browser. The Table Browser, Data Integrator, and download server are not available +for this track. </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>. </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> <h2>References</h2> <p> All of Us Research Program Genomics Investigators. <a href="https://doi.org/10.1038/s41586-023-06957-x" target="_blank"> Genomic data in the All of Us Research Program</a>. <em>Nature</em>. 2024 Mar;627(8003):340-346. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38374255" target="_blank">38374255</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10937371/" target="_blank">PMC10937371</a> </p>