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/sfariSparkExomes.html src/hg/makeDb/trackDb/human/sfariSparkExomes.html index a7a30e0d2d8..27e11ff2610 100644 --- src/hg/makeDb/trackDb/human/sfariSparkExomes.html +++ src/hg/makeDb/trackDb/human/sfariSparkExomes.html @@ -3,37 +3,33 @@ The <a href="https://sparkforautism.org/" target="_blank">Simons Foundation Autism Research Initiative (SFARI)</a> recruited a large cohort of families with autistic children who provided DNA samples and phenotypes. 54,558 families, parents and their children were sequenced, a total of 142,357 individuals with whole-exome (WES) and 12,519 with whole-genome sequencing (WGS). The data contains 32,559 trios and 8,895 quads (one sibling without autism), and 824 twins. </p> <p> The same frequencies shown here are also available publicly on the <a href="https://genomes.sfari.org/" target="_blank">SFARI Genome Browser</a>. See (SPARK et al, Neuron 2018) for details. </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>sfariSparkExomes</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> Allele frequencies can also be displayed on the <a href="https://genomes.sfari.org/" target="_blank">SFARI Genome Browser</a>. Full CRAMs and VCFs with genotypes are available from <a href="https://base.sfari.org/" target="_blank">SFARI Base</a>. They require a data access request, which is usually reviewed quickly. More information is available in the <a href="https://cohorts-cdn.simonsfoundation.org/spark/researcher_packets/SPARK_SFARI_Researcher_Welcome_Packet.pdf" target="_blank">SPARK Welcome Packet</a>. </p> <h2>Methods</h2> <p>The genome browser track project was approved by the Simons Foundation under request