2731937b048d40737f10ece92ceff7bd5251d5a9 gperez2 Mon Aug 22 16:44:12 2022 -0700 Updating news for dbSNP build 155 tracks, refs #27751 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 09924ec..abb3b05 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,69 @@ <div class="col-sm-3"> <ul> <li><a href="#2006">2006 News</a></li> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2001">2001</a>-<a href="#2002">2002 News</a></li> </ul> </div> </div> </div> <!-- ============= 2022 archived news ============= --> <a name="2022"></a> +<a name="082222"></a> +<h2>Aug. 22, 2022 dbSNP build 155 tracks for hg19 and hg38</h2> +<p> +We are pleased to announce the release of +<a href="https://www.ncbi.nlm.nih.gov/SNP/" target="_blank">NCBI's dbSNP</a> build 155 data for +<a href="../cgi-bin/hgTrackUi?db=hg38&g=dbSnp155Composite" target="_blank">GRCh38/hg38</a> and +<a href="../cgi-bin/hgTrackUi?db=hg19&g=dbSnp155Composite" target="_blank">GRCh37/hg19</a> human +assemblies. The release reaches a new milestone of over 1 billion RefSNP (rs) records. For hg38 +(GRCh38), approximately 998 million distinct variants (RefSNP clusters with rs# ids) have been +mapped to more than 1.06 billion genomic locations including alternate haplotype and fix patch +sequences. dbSNP remapped variants from hg38 to hg19 (GRCh37); approximately 981 million distinct +variants were mapped to more than 1.02 billion genomic locations including alternate haplotype and +fix patch sequences (not all of which are included in UCSC's hg19).</p> + +<p> +dbSNP build 155 is composed of 5 subtracks: +<ul> + <li><b>Common dbSNP(155)</b> - Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants</li> + <li><b> ClinVar dbSNP(155)</b> - Short Genetic Variants in ClinVar</li> + <li><b>Mult. dbSNP(155)</b> - Short Genetic Variants that map to multiple genomic loci</li> + <li><b>All dbSNP(155)</b> - All Short Genetic Variants</li> + <li><b>Map Err dbSnp(155)</b> - Mappings with Inconsistent Coordinates</li> +</ul></p> + +<h3>Data Access</h3> +<p> +The complete data can be found across two separate directories in our download server, a bigBed file +(bigDbSnp) for <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hg19/snp/">hg19</a> +and <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/">hg38</a>, and a +<a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hgFixed/dbSnp/">shared secondary +details file</a> which holds additional variant details.<p> +</p> + +<p> +We would like to thank the dbSNP group at NCBI for providing access to these data. We would also +like to thank Galt Barber, Angie Hinrichs, and Gerardo Perez for their efforts on this release. +</p> + + <a name="080222"></a> <h2>Aug. 08, 2022 New GENCODE gene tracks: Human V41 (hg19/hg38) - Mouse VM30 (mm39)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="https://www.ensembl.info/2022/05/31/whats-coming-in-ensembl-release-107-ensembl-genomes-54/" target="_blank">Ensembl 107</a>, for three assemblies: <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=wgEncodeGencodeV41lift37">hg19/GRCh37</a>, <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=wgEncodeGencodeV41">hg38/GRCh38</a>, and <a target="_blank" href="/cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM30">mm39/GRCm39</a>. For human, the GENCODE V41 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the following tracks:</p> <ul>