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/topmed.html src/hg/makeDb/trackDb/human/topmed.html index 3b8048cbaf7..d67f8a75e61 100644 --- src/hg/makeDb/trackDb/human/topmed.html +++ src/hg/makeDb/trackDb/human/topmed.html @@ -1,37 +1,33 @@ <h2>Description</h2> <p> <a href="https://topmed.nhlbi.nih.gov/" target="_blank">NHLBI TOPMed</a> (Trans-Omics for Precision Medicine) is a program launched by the U.S. National Heart, Lung, and Blood Institute that integrates whole-genome sequencing with molecular, clinical, and environmental data from large, well-phenotyped cohorts. Its goal is to uncover the biological mechanisms underlying heart, lung, blood, and sleep disorders to advance precision medicine and improve population health. Freeze 10 contains 868,581,653 variants from 150,899 whole genomes. </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>topmed</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> -VCFs with summarized allele frequencies are also available from +VCFs with summarized allele frequencies are available from the <a href="https://bravo.sph.umich.edu/" target="_blank">TOPMED BRAVO website</a>. They require a login. The VCFs were downloaded from <a href="https://bravo.sph.umich.edu/terms.html" target="_blank">BRAVO</a>. </p> <h2>Methods</h2> <p> TOPMed whole genome sequencing was performed at multiple NHLBI-funded sequencing centers using PCR-free library preparation with 150 bp paired-end reads on Illumina short-read platforms, targeting ≥30x mean coverage. Reads were aligned to the GRCh38 reference genome (hs38DH, including decoy sequences) using BWA-MEM, followed by duplicate marking with Picard MarkDuplicates and base quality score recalibration (BQSR) with GATK. Variant calling was performed using the TOPMed GotCloud pipeline (developed at the Center for Statistical Genetics, University of Michigan), comprising: (1) per-sample candidate variant detection with <code>vt discover2</code> and normalization with <code>vt normalize</code>; (2) cross-sample variant site