9f25bb947c005d453ff47f8beac29dc18afde9c3 jnavarr5 Fri Mar 13 15:32:43 2026 -0700 Staging the announcement for the gnomAD coverage tracks, refs #37036 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index f86cda14dbd..9b8b4f21925 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,109 @@ <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2026"></a> +<a name="031326"></a> +<h2>Mar. 13, 2026 gnomAD v4 Exome and v3 Genome coverage tracks for hg38</h2> +<p> +We are pleased to announce the release of two new coverage tracks from the +<a href="https://gnomad.broadinstitute.org/" target="_blank">Genome Aggregation Database +(gnomAD)</a> on the human GRCh38/hg38 assembly. These tracks are part of the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants">Genome Aggregation Database (gnomAD)</a> +track collection. +</p> + +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomad4ExomeCoverage">gnomAD v4 Exome Coverage</a> +track displays per-base sequencing coverage statistics derived from the gnomAD v4.0 +exome callset. Coverage was computed across all gnomAD v4 exome samples using gVCFs +produced with a 3-bin blocking scheme based on reference genotype quality +(< Q20 and ≥ Q20). Note that there is no gnomAD v4 genome coverage track because +the genome samples were unchanged from v3. The track contains the following subtracks: +</p> + +<ul> + <li> + <b>Mean Coverage</b> – mean read depth across exome samples at each base + position + </li> + <li> + <b>Median Coverage</b> – median read depth across exome samples at each base + position + </li> + <li> + <b>Sample % > 1X, 5X, 10X, 15X, 20X, 25X, 30X, 50X, 100X</b> – + the percentage of exome samples with read depth at or above the indicated + coverage threshold at each base position + </li> +</ul> + +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomad3Coverage">gnomAD v3 Genome Coverage</a> +track displays equivalent per-base coverage statistics computed from 71,702 gnomAD +v3.0.1 whole-genome samples, also using gVCFs and the same 3-bin quality blocking +scheme. Note that there is no gnomAD v3 exome coverage track because gnomAD v3 was a +genome-only release. The track contains the following subtracks: +</p> + +<ul> + <li> + <b>Mean Coverage</b> – mean read depth across genome samples at each base + position + </li> + <li> + <b>Median Coverage</b> – median read depth across genome samples at each + base position + </li> + <li> + <b>Sample % > 1X, 5X, 10X, 15X, 20X, 25X, 30X, 50X, 100X</b> – + the percentage of genome samples with read depth at or above the indicated + coverage threshold at each base position + </li> +</ul> + +<p> +For both tracks, clicking on a feature opens a details page that shows calculated +sample coverage percentages across the sequence range visible in the browser window. +Coverage data files in <a href="/goldenPath/help/bigWig.html">bigWig</a> +format are available from our +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/">download server</a> +in the <code>coverage/</code> subdirectory, and data can also be explored interactively +using the <a href="/cgi-bin/hgTables">Table Browser</a> or +<a href="/cgi-bin/hgIntegrator">Data Integrator</a>. +Raw data are also available directly from the gnomAD +<a href="https://gnomad.broadinstitute.org/downloads">downloads page</a>. +</p> + +<p> +We would like to thank the +<a href="https://gnomad.broadinstitute.org/about">Genome Aggregation Database +Consortium</a> for making the data public. We also would like to thank Max Haeussler and Jairo +Navarro Gonzalez for the creation and release of the UCSC Genome Browser tracks. +</p> + <a name="022426"></a> <h2>Feb. 24, 2026 Updates to the Genome Browser Gateway Page and Assembly Search</h2> <p> We are excited to announce new <b>Recent Genomes</b> and <b>Connected Hub Assemblies</b> lists on the <a href="/cgi-bin/hgGateway" target="_blank">Gateway page</a>, along with improvements to genome assembly searching across the Genome Browser. The genome assemblies search box is now also available on other pages and tools, including <a href="/cgi-bin/hgBlat" target="_blank">BLAT</a>, <a href="/cgi-bin/hgPcr" target="_blank">In-Silico PCR</a>, <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a>, <a href="/cgi-bin/hgLiftOver" target="_blank">LiftOver</a>, <a href="/cgi-bin/hgCustom" target="_blank">Custom Tracks</a>, and others. </p> <div class="text-center">