125b79e5c4908d8c0015c53e16db2003dd02a7c5 jnavarr5 Mon Jan 20 17:05:33 2020 -0800 Announcing the 1000 Genomes Project variants track for hg38, refs #21805 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 80a15c4..ee0a105 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -38,30 +38,56 @@ </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2004">2004 News</a></li> <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> <!-- ============= 2019 archived news ============= --> <a name="2019"></a> +<a name="012020"></a> +<h2>Jan. 20, 2020 1000 Genomes Project Phase 3 variants now available for human + (GRCh38/hg38)</h2> +<p> +We are happy to announce the release of the 1000 Genomes Phase 3 Integrated Variant Calls from the +<a href="https://www.internationalgenome.org/" target="_blank">International Genome Sample Resource +(IGSR)</a> for human +(<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=tgpPhase3" target="_blank">GRCh38/hg38</a>). This +track shows approximately 73 million single nucleotide variants (SNVs) and 5 million short insertions/deletions (indels) +produced by the IGSR from sequence data generated by the 1000 Genomes Project in its Phase 3 +sequencing of 2,504 genomes from 16 populations worldwide. The genomes of 2,504 individuals were +sequenced using both whole-genome sequencing (mean depth = 7.4x) and targeted exome sequencing +(mean depth = 65.7x). Sequence reads were aligned to the reference genome using alt-aware BWA-MEM +(<a href="https://academic.oup.com/gigascience/article/6/7/gix038/3836916" +target="_blank">Zheng-Bradley et al.</a>). Variant discovery and quality control were performed as +described in (<a href="https://wellcomeopenresearch.org/articles/4-50" target="_blank">Lowy-Gallego +et al.</a>).</p> +<p> +Variants were called on the autosomes (chromosomes 1 through 22) and on the Pseudo-Autosomal Regions +(PARs) of chromosome X. Therefore this track has no annotations on alternate haplotype sequences, +fix patches, chromosome Y and the non-PAR portion (the majority) of chromosome X.</p> +<p> +We would like to thank the IGSR for making these variant calls freely available. We would also like +to thank Angie Hinrichs and Jairo Navarro for their efforts in creating and reviewing this track. +</p> + <a name="121319"></a> <h2>Dec. 13, 2019 New dbSNP pipeline: dbSNP b153 release, bigDbSnp track type</h2> <p> We are pleased to announce a new dbSNP pipeline, along with the first new dataset: dbSNP b153 for <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&g=dbSnp153Composite">hg19</a> and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&g=dbSnp153Composite">hg38</a>.</p> <p> dbSNP has seen an <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/02/dbsnp-database-doubles-size-twice-13-months/"> explosive growth</a> in recent releases, from roughly 324 million variants in <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/dbsnps-human-build-150-has-doubled-the-amount-of-refsnp-records/"> build 150</a>, to over 700 million variants in the latest build b153. In an effort to continue providing efficient access to this data, dbSNP has redesigned their <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/07/07/dbsnp-redesign-supports-future-data-expansion/"> architecture and data flow</a>. We have also taken this opportunity to redesign our dbSNP