630550c8e3eef4679f6cfb1e89af12c1a05875d5 jnavarr5 Wed Sep 24 18:00:04 2025 -0700 Adding an image to the news post. Fixing the g= parameter for the hs1 assembly, refs #34120 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index b55dd14a8c5..12f0401fdbc 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -87,45 +87,55 @@ variant calls for clinical or research human samples. It shows regions that are easy to sequence, rather than those that are problematic. The data was derived from the HPRC assemblies, and this track presents the 151b-easy panmask set.</p> <p> We would like to thank the <a href="https://hlilab.github.io/" target="_blank">HLi lab</a> at Harvard Medical School for making this data available. We would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.</p> --> <a name="092425"></a> <h2>Sep. 24, 2025 CoLoRSdb Small and Structure variants for hg38 and hs1</h2> <p> We are excited to announce the release of the CoLoRSdb Small and Structural Variant tracks for the human assemblies -<a href="/cgi-bin/hgTrackUi?db=hg38&g=colorsDb&position=default" target="_blank">GRCh38/hg38</a> and -<a href="/cgi-bin/hgTrackUi?db=hs1&g=colorsDb&position=default" target="_blank">CHM13/hs1</a>. These -tracks provide a comprehensive catalog of genetic variation discovered through long-read whole -genome sequencing, contributed by the international +<a href="/cgi-bin/hgTrackUi?db=hg38&g=structuralVariants&position=default" target="_blank">GRCh38/hg38</a> and +<a href="/cgi-bin/hgTrackUi?db=hs1&g=hub_3671779_structuralVariants&position=default" +target="_blank">CHM13/hs1</a>. These tracks provide a comprehensive catalog of genetic variation +discovered through long-read whole genome sequencing, contributed by the international <a href="https://colorsdb.org" target="_blank">Consortium of Long Read Sequencing (CoLoRS)</a>. The small variant tracks (DeepVariant + GLnexus) contain single nucleotide polymorphisms (SNPs) and short indels, while the structural variant tracks (pbsv + Jasmine) display larger events including insertions, deletions, and inversions. Long-read sequencing technology improves sensitivity in repetitive regions and provides more precise breakpoint resolution than short-read approaches, enabling accurate visualization of complex loci in the Genome Browser.</p> <p> Each track includes allele frequency and sample count annotations, with additional filtering options for variant size and type. Users can click on individual variants to view detailed metadata, such as allele counts, homozygous/heterozygous call distributions, and Hardy-Weinberg equilibrium values. </p> + +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/jnavarr5/CoLoRSdb_announcement"> + <img src="../images/newsArchImages/CoLoRSdb.png" + alt="CoLoRSdb track with the mouseover tooltip on the DEL-159bp item." width='65%'> + <p class="gbsCaption"> + <em>Genome Browser screenshot of the CoLoRSdb tracks with the mouseover tooltip on the DEL-159bp + item.</em> + </p></a> +</div> <p> We would like to thank Mike Schatz, Evan Eichler, and all <a href="https://colorsdb.org/membership" target="_blank">CoLoRSdb investigators</a> for generating and making the data publicly available. We would also like to thank Karen Wang and Jairo Navarro Gonzalez for the creation and release of these tracks. </p> <a name="091925"></a> <h2>Sep. 19, 2025 Developmental Disorders Gene2Phenotype (DDG2P) for hg38 and hg19</h2> <p> We are pleased to announce the release of the <a href="https://www.deciphergenomics.org/ddd/ddgenes" target="_blank">Developmental Disorders Genotype-to-Phenotype (DDG2P)</a> track for <a href="/cgi-bin/hgTrackUi?db=hg19&g=ddg2p&position=default" target="_blank">hg19</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&g=ddg2p&position=default" target="_blank">hg38</a>. The DDG2P track displays genes associated with severe developmental disorders. The track can be used to