5172b8655d2ef742e9bf918cedb3fa746d50d0f0 gperez2 Thu Sep 25 11:21:58 2025 -0700 Uncommenting the Panmask track newsarch announcement, refs #36293 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 07d4bd84763..deaed62ef58 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,60 +51,58 @@ </div> <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="2025"></a> -<!-- <a name="092525"></a> <h2>Sep. 25, 2025 Panmask Easy 151b Regions track for hg38</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=panmask151b" target="_blank">Panmask Easy 151b Regions</a> track for hg38. This new track is available in the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=problematicSuper" target="_blank">Problematic Regions superTrack</a>. The track contains a set of sample-agnostic easy regions where short-read variant calling reaches high accuracy. Easy regions are derived for variant filtration agnostic to individual samples. They are genomic intervals where general variant callers achieve high accuracy without sophisticated filtering.</p> <p class="text-center"> <img src="../../images/newsArchImages/panmask.png" alt="Panmask Easy 151b Regions track for the BRCA1 exon 19" width='75%'></p> <p> The pm151 regions are used to filter spurious variant calls in centromeres, long repeats, and other genomic regions where short-read mapping is often problematic. They cover 88.2% of hg38, 92.2% of coding regions, and 96.3% of ClinVar pathogenic variants. The track can be used to filter 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=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,