3a506cd303b10c3c81e3196e990d4487f8757e2e gperez2 Tue Nov 5 11:07:01 2024 -0800 Announcing the release of the difficult regions from GIAB tracks, refs #32715 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 70bee39..eaa7a58 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,55 @@ <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> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="110424"></a> +<h2>Nov. 4, 2024 GIAB Problematic Regions tracks for human (hg38 and hs1)</h2> +<p> +We are pleased to announce the release of the +<a href="https://www.nist.gov/programs-projects/genome-bottle" target="_blank" + >Genome in a Bottle (GIAB)</a> Problematic Regions tracks for the +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=problematicGIAB" target="_blank">hg38</a> +and +<a href="/cgi-bin/hgTrackUi?db=hub_25071_hs1&position=default&g=hub_25071_problematic" +target="_blank">hs1</a> human assemblies. The tracks provide stratifications of the genome to +evaluate variant calls in complex regions and it is designed for use with Global Alliance for +Genomic Health (GA4GH) benchmarking tools like +<a href="https://github.com/Illumina/hap.py" target="_blank">hap.py</a>. It includes regions with +low complexity, segmental duplications, functional regions, and difficult-to-sequence areas. The +GIAB Problematic Regions composite track consists of four subtracks:</p> +<ul> + <li><b>All difficult regions</b> – Genome In a Bottle: all difficult regions + <li><b>LowMap+SegDup</b> – Genome In a Bottle: lowMap+SegDup regions + <li><b>Not difficult regions</b> – Genome In a Bottle: not difficult regions + <li><b>Not lowMap+SegDup</b> – Genome In a Bottle: not lowMap+SegDup mapping regions +</ul> +<p> +We would like to thank the Genome in a Bottle Consortium, Telomere-to-Telomere Consortium and NIST +for providing this data. We would also like to thank Megna Chalamala, Jairo Navarro, and Gerardo +Perez for the creation and release of these tracks.</p> <a name="102324"></a> <h2>Oct. 23, 2024 New GENCODE "KnownGene" V47 for human (hg38) and VM36 for mouse (mm39)</h2> <p> We are pleased to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=knownGene">GENCODE V47 (hg38)</a> and the <a href="/cgi-bin/hgTrackUi?db=mm39&position=default&g=knownGene">GENCODE VM36 (mm39)</a> gene tracks. The GENCODE "KnownGene" V47 and VM36 gene tracks were built using a UCSC pipeline (KnownGene) and the GENCODE comprehensive gene set to generate high-quality manual annotations merged with evidence-based automated annotations. The GENCODE "KnownGene" tracks are our default gene tracks, which have extensive associations to external sources. This allows for additional metadata on every item as well as external links. The track description pages contain options for configuring the display, such as showing non-coding genes, splice variants, and pseudogenes.</p>