a63f1ceba1c9349722814de6b6c6f1f326f0f93f dschmelt Thu Sep 24 18:21:36 2020 -0700 Adding announce for COVID GWAS and Trios, Removing 404 link refs #26129 26076 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index bbc0632..a7d6102 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -44,62 +44,95 @@ <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> <a name="092520"></a> <h2>New data and visualization types: Covid GWAS (Lollypop) and Family Trios (VCF Trios)</h2> <h3>Covid GWAS meta-analysis (Lollypop format)</h3> <p> -We are happy to announce the COVID-19 GWAS tracks both popular human genomes -(<a href="../../cgi-bin/hgTracksUi?db=hg19&g=covidHgiGwas">GRCh37/hg19</a> and -<a href="../../cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas">GRCh38/hg38</a>). +We are happy to announce the COVID-19 GWAS tracks in /both popular human genomes +(<a href="../../cgi-bin/hgGateway?db=hg19">GRCh37/hg19</a> and +<a href="../../cgi-bin/hgGateway?db=hg38">GRCh38/hg38</a>). These tracks show GWAS meta-analyses from the <a href="https://www.covid19hg.org/" target="_blank"> COVID-19 Host Genetics Initiative (HGI)</a>, a collaborative effort to analyze and share viral host -genetics reseach. This track brings together data from 26 GWAS studies and aims to identify +genetics research. This track brings together data from 26 GWAS studies and aims to identify genetic determinants of SARS-CoV-2 infection susceptibility and disease severity. </p> - +<p> These data are shown in our new Lollypop visualization in order to show the added dimensions of effect size and p-value in addition to location. Filters are also -available for these variables and the number of studies. For more information on these +available for these variables and the number of studies. Custom tracks using the +lollypop format is not yet available. For more information on these datasets, please read the track description page and try the interactive visualization for yourself:</p> <ul> -<li><a href="../../cgi-bin/hgTracksUi?db=hg19&g=covidHgiGwas">GRCh37/hg19</a></li> -<li><a href="../../cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas">GRCh38/hg38</a></li> +<li><a href="../../cgi-bin/hgTrackUi?db=hg19&g=covidHgiGwas">COVID-19 GWAS on GRCh37/hg19</a></li> +<li><a href="../../cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas">COVID-19 GWAS on GRCh38/hg38</a></li> </ul> -#PICTURE +<div class="text-center"> +<a href="../../cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=dschmelt&hgS_otherUserSessionName=covidGwas"> +<img width="80%" height="80%" +src="../../images/CovidGWAS.png" alt="The COVID-19 GWAS track shows variants as lollypops, +with the colored head showing the p-value and the height of the stick showing effect size."></a> +</div> <p>Our gratitude goes to the COVID-19 Host Genetics Initiative contributors and project leads for making this data available and Kumar Veerapen at the Broad for their input during track -development. We would also like to thank Kate Rosenbloom, Daniel Schmelter, and Ana Benet for +development. We would also like to thank Kate Rosenbloom, Daniel Schmelter, and Ana Benet-Pages for developing, staging, and documenting this track.</p> <h3>1000 Genomes Family Trios (Phased VCFs)</h3> +<p> +We are happy to share a new data set, 1000 Genomes Trios on hg38, and a visualization tool for +displaying chromosome phased VCFs and family inheritance patterns. This track shows phased +variants from seven trios of parents and child across different regions. +You can infer which parent passed on which variant and identify +possible de-Novo variants. The data was produced by <a +href="https://www.internationalgenome.org/" target="_blank">International Genome Sample +Resource (IGSR)</a> from sequence data generated by the +<a href="https://www.internationalgenome.org/about" target="_blank">1000 Genomes Project</a>. +For more information on the 1000 Genomes Trios track and the VCF Trio format, please visit +the track description page and VCF help page: +</p> +<ul> +<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=tgpTrios"> +1000 Genomes Trios on GRCh38/hg38</a></li> +<li><a href="https://genome.ucsc.edu/goldenPath/help/vcf.html#trio">VCF track format</a></li> +</ul> + +<div class="text-center"> +<a href="../../cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=dschmelt&hgS_otherUserSessionName=tgpTrios"> +<img width="80%" height="80%" +src="../../images/trioExample.png" alt="3 VCF Phased Trio tracks along with the GENCODE +v32 genes from the Human/GRCh38 assembly. Each of two diploid haplotypes for each individual +in a trio is drawn as a black lane, with snps as vertical ticks on the haplotype they fall on. +Ticks are shaded blue,red,green or black according to their predicted functional effect."></a> +</div> - - - +<p> +We would like to thank the IGSR and 1000 Genomes Project teams and contributors for +doing the research and making their data accessible. We would also like to thank Chris Lee, +Daniel Schmelter, and Angie Hinrichs for designing, developing, and releasing this track.</p> <a name="091120"></a> <h2>Sept. 11, 2020 UCSC LiftOver and NCBI Remap alignments for human (hg38/hg19)</h2> <p> We are proud to announce the release of UCSC LiftOver and NCBI Remap alignments for human (<a href="../../cgi-bin/hgTrackUi?db=hg19&g=liftHg38">GRCh37/hg19</a> and <a href="../../cgi-bin/hgTrackUi?db=hg38&g=liftHg19">GRCh38/hg38</a>). These alignments are contained in a composite track with three subtracks, one for UCSC LiftOver and two for NCBI alignments. </p> <ul> <li>UCSC liftOver alignments to hg19/hg38</li> <li>NCBI ReMap alignments to hg19/hg38</li> <li>NCBI ReMap alignments to hg19/hg38, joined by axtChain</li> </ul> @@ -4115,31 +4148,31 @@ <p> The <a href="../../cgi-bin/hgTrackUi?db=hg38&g=mappability" target="_blank">Mappability</a> supertrack contains two composite tracks, <a href="../../cgi-bin/hgTrackUi?db=hg38&g=mappability" target="_blank">Bismap</a> and <a href="../../cgi-bin/hgTrackUi?db=hg38&g=mappability" target="_blank">Umap</a>. Both Umap and Bismap tracks contain single-read and multi-read mappability tracks for four different read lengths: 24 bp, 36 bp, 50 bp, and 100 bp. You can use these tracks for many purposes, including filtering unreliable signal from sequencing assays. The Bismap track can help filter unreliable signal from sequencing assays involving bisulfite conversion, such as whole-genome bisulfite sequencing or reduced representation bisulfite sequencing.</p> <p> For greater detail and explanatory diagrams, see the <a href="https://www.biorxiv.org/content/early/2016/12/20/095463" target="_blank">preprint</a>, the <a href="http://bismap.hoffmanlab.org/" target="_blank">Umap and Bismap project website</a>, -or the <a href="https://bitbucket.org/hoffmanlab/umap" target="_blank">Umap and Bismap software +or the <a href="https://github.com/hoffmangroup/umap" target="_blank">Umap and Bismap software documentation</a>.</p> <p> A huge thank you to <a href="https://sites.google.com/site/anshulkundaje/" target="_blank">Anshul Kundaje</a> (Stanford University) who created the original Umap software in MATLAB and Mehran Karimzadeh (<a href="https://hoffmanlab.org/" target="_blank">Michael Hoffman lab</a>, Princess Margaret Cancer Centre) who implemented the Python version of Umap and added features, including Bismap. Thanks to Hiram Clawson, Chris Eisenhart, and Jairo Navarro of the UCSC Genome Browser. <!-- ============= 2017 archived news ============= --> <a name="2017"></a> <a name="121917"></a> <h2>Dec. 19, 2017 New genome browser: Bonobo, panPan2 (<em>Pan paniscus</em>)</h2>