06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 219f4e3..b097b8a 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,353 @@ </div> <div class="col-sm-3"> <ul> <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="#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="120220"></a> +<h2>Dec. 2, 2020 New and updated UniProt tracks for 117 assemblies</h2> +<p> +We are pleased to announce new and updated +<a href="https://www.uniprot.org/" target="_blank"</a>UniProt tracks</a> for the +following assemblies:</p><br> +<div class="container"> + <div class="row"> + <div class="col-sm-4"> + <ul> + <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam1&g=uniprot" + target=_blank>(anoGam1)</a></li> + <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam3&g=uniprot" + target=_blank>(anoGam3)</a></li> + <li>A. mellifera <a href="../cgi-bin/hgTrackUi?db=apiMel2&g=uniprot" + target=_blank>(apiMel2)</a></li> + <li>African clawed frog <a href="../cgi-bin/hgTrackUi?db=xenLae2&g=uniprot" + target=_blank>(xenLae2)</a></li> + <li>Alpaca <a href="../cgi-bin/hgTrackUi?db=vicPac2&g=uniprot" + target=_blank>(vicPac2)</a></li> + <li>American alligator <a href="../cgi-bin/hgTrackUi?db=allMis1&g=uniprot" + target=_blank>(allMis1)</a></li> + <li>Armadillo <a href="../cgi-bin/hgTrackUi?db=dasNov3&g=uniprot" + target=_blank>(dasNov3)</a></li> + <li>Atlantic cod <a href="../cgi-bin/hgTrackUi?db=gadMor1&g=uniprot" + target=_blank>(gadMor1)</a></li> + <li>Baboon <a href="../cgi-bin/hgTrackUi?db=papAnu4&g=uniprot" + target=_blank>(papAnu4)</a></li> + <li>Baboon <a href="../cgi-bin/hgTrackUi?db=papHam1&g=uniprot" + target=_blank>(papHam1)</a></li> + <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=uniprot" + target=_blank>(bisBis1)</a></li> + <li>Bonobo <a href="../cgi-bin/hgTrackUi?db=panPan3&g=uniprot" + target=_blank>(panPan3)</a></li> + <li>Brown kiwi <a href="../cgi-bin/hgTrackUi?db=aptMan1&g=uniprot" + target=_blank>(aptMan1)</a></li> + <li>Budgerigar <a href="../cgi-bin/hgTrackUi?db=melUnd1&g=uniprot" + target=_blank>(melUnd1)</a></li> + <li>Bushbaby <a href="../cgi-bin/hgTrackUi?db=otoGar3&g=uniprot" + target=_blank>(otoGar3)</a></li> + <li>C. brenneri <a href="../cgi-bin/hgTrackUi?db=caePb2&g=uniprot" + target=_blank>(caePb2)</a></li> + <li>C. briggsae <a href="../cgi-bin/hgTrackUi?db=cb3&g=uniprot" + target=_blank>(cb3)</a></li> + <li>C. elegans <a href="../cgi-bin/hgTrackUi?db=ce10&g=uniprot" + target=_blank>(ce10)</a></li> + <li>C. elegans <a href="../cgi-bin/hgTrackUi?db=ce11&g=uniprot" + target=_blank>(ce11)</a></li> + <li>C. elegans <a href="../cgi-bin/hgTrackUi?db=ce6&g=uniprot" + target=_blank>(ce6)</a></li> + <li>C. intestinalis <a href="../cgi-bin/hgTrackUi?db=ci3&g=uniprot" + target=_blank>(ci3)</a></li> + <li>C. japonica <a href="../cgi-bin/hgTrackUi?db=caeJap1&g=uniprot" + target=_blank>(caeJap1)</a></li> + <li>C. remanei <a href="../cgi-bin/hgTrackUi?db=caeRem3&g=uniprot" + target=_blank>(caeRem3)</a></li> + <li>Cat <a href="../cgi-bin/hgTrackUi?db=felCat9&g=uniprot" + target=_blank>(felCat9)</a></li> + <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal6&g=uniprot" + target=_blank>(galGal6)</a></li> + <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro6&g=uniprot" + target=_blank>(panTro6)</a></li> + <li>Chinese hamster <a href="../cgi-bin/hgTrackUi?db=criGriChoV2&g=uniprot" + target=_blank>(criGriChoV2)</a></li> + <li>Chinese pangolin <a href="../cgi-bin/hgTrackUi?db=manPen1&g=uniprot" + target=_blank>(manPen1)</a></li> + <li>Coelacanth <a href="../cgi-bin/hgTrackUi?db=latCha1&g=uniprot" + target=_blank>(latCha1)</a></li> + <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau8&g=uniprot" + target=_blank>(bosTau8)</a></li> + <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau9&g=uniprot" + target=_blank>(bosTau9)</a></li> + <li>Crab-eating macaque <a href="../cgi-bin/hgTrackUi?db=macFas5&g=uniprot" + target=_blank>(macFas5)</a></li> + <li>D. ananassae <a href="../cgi-bin/hgTrackUi?db=droAna2&g=uniprot" + target=_blank>(droAna2)</a></li> + <li>D. erecta <a href="../cgi-bin/hgTrackUi?db=droEre1&g=uniprot" + target=_blank>(droEre1)</a></li> + <li>D. grimshawi <a href="../cgi-bin/hgTrackUi?db=droGri1&g=uniprot" + target=_blank>(droGri1)</a></li> + <li>D. melanogaster <a href="../cgi-bin/hgTrackUi?db=dm6&g=uniprot" + target=_blank>(dm6)</a></li> + <li>D. mojavensis <a href="../cgi-bin/hgTrackUi?db=droMoj2&g=uniprot" + target=_blank>(droMoj2)</a></li> + <li>D. persimilis <a href="../cgi-bin/hgTrackUi?db=droPer1&g=uniprot" + target=_blank>(droPer1)</a></li> + <li>D. pseudoobscura <a href="../cgi-bin/hgTrackUi?db=dp3&g=uniprot" + target=_blank>(dp3)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>D. sechellia <a href="../cgi-bin/hgTrackUi?db=droSec1&g=uniprot" + target=_blank>(droSec1)</a></li> + <li>D. simulans <a href="../cgi-bin/hgTrackUi?db=droSim1&g=uniprot" + target=_blank>(droSim1)</a></li> + <li>D. virilis <a href="../cgi-bin/hgTrackUi?db=droVir2&g=uniprot" + target=_blank>(droVir2)</a></li> + <li>D. yakuba <a href="../cgi-bin/hgTrackUi?db=droYak2&g=uniprot" + target=_blank>(droYak2)</a></li> + <li>Dog <a href="../cgi-bin/hgTrackUi?db=canFam4&g=uniprot" + target=_blank>(canFam4)</a></li> + <li>Dolphin <a href="../cgi-bin/hgTrackUi?db=turTru2&g=uniprot" + target=_blank>(turTru2)</a></li> + <li>Ebola virus <a href="../cgi-bin/hgTrackUi?db=eboVir3&g=uniprot" + target=_blank>(eboVir3)</a></li> + <li>Elephant <a href="../cgi-bin/hgTrackUi?db=loxAfr3&g=uniprot" + target=_blank>(loxAfr3)</a></li> + <li>Elephant shark <a href="../cgi-bin/hgTrackUi?db=calMil1&g=uniprot" + target=_blank>(calMil1)</a></li> + <li>Ferret <a href="../cgi-bin/hgTrackUi?db=musFur1&g=uniprot" + target=_blank>(musFur1)</a></li> + <li>Fugu <a href="../cgi-bin/hgTrackUi?db=fr3&g=uniprot" + target=_blank>(fr3)</a></li> + <li>Garter snake <a href="../cgi-bin/hgTrackUi?db=thaSir1&g=uniprot" + target=_blank>(thaSir1)</a></li> + <li>Gibbon <a href="../cgi-bin/hgTrackUi?db=nomLeu3&g=uniprot" + target=_blank>(nomLeu3)</a></li> + <li>Golden eagle <a href="../cgi-bin/hgTrackUi?db=aquChr2&g=uniprot" + target=_blank>(aquChr2)</a></li> + <li>Golden snub-nosed monkey <a href="../cgi-bin/hgTrackUi?db=rhiRox1&g=uniprot" + target=_blank>(rhiRox1)</a></li> + <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor6&g=uniprot" + target=_blank>(gorGor6)</a></li> + <li>Green monkey <a href="../cgi-bin/hgTrackUi?db=chlSab2&g=uniprot" + target=_blank>(chlSab2)</a></li> + <li>Guinea pig <a href="../cgi-bin/hgTrackUi?db=cavPor3&g=uniprot" + target=_blank>(cavPor3)</a></li> + <li>Hedgehog <a href="../cgi-bin/hgTrackUi?db=eriEur2&g=uniprot" + target=_blank>(eriEur2)</a></li> + <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=uniprot" + target=_blank>(equCab3)</a></li> + <li>Human <a href="../cgi-bin/hgTrackUi?db=hg19&g=uniprot" + target=_blank>(hg19)</a></li> + <li>Human <a href="../cgi-bin/hgTrackUi?db=hg38&g=uniprot" + target=_blank>(hg38)</a></li> + <li>Kangaroo rat <a href="../cgi-bin/hgTrackUi?db=dipOrd1&g=uniprot" + target=_blank>(dipOrd1)</a></li> + <li>Lamprey <a href="../cgi-bin/hgTrackUi?db=petMar3&g=uniprot" + target=_blank>(petMar3)</a></li> + <li>Lancelet <a href="../cgi-bin/hgTrackUi?db=braFlo1&g=uniprot" + target=_blank>(braFlo1)</a></li> + <li>Lizard <a href="../cgi-bin/hgTrackUi?db=anoCar2&g=uniprot" + target=_blank>(anoCar2)</a></li> + <li>Malayan flying lemur <a href="../cgi-bin/hgTrackUi?db=galVar1&g=uniprot" + target=_blank>(galVar1)</a></li> + <li>Manatee <a href="../cgi-bin/hgTrackUi?db=triMan1&g=uniprot" + target=_blank>(triMan1)</a></li> + <li>Marmoset <a href="../cgi-bin/hgTrackUi?db=calJac3&g=uniprot" + target=_blank>(calJac3)</a></li> + <li>Medaka <a href="../cgi-bin/hgTrackUi?db=oryLat2&g=uniprot" + target=_blank>(oryLat2)</a></li> + <li>Medium ground finch <a href="../cgi-bin/hgTrackUi?db=geoFor1&g=uniprot" + target=_blank>(geoFor1)</a></li> + <li>Megabat <a href="../cgi-bin/hgTrackUi?db=pteVam1&g=uniprot" + target=_blank>(pteVam1)</a></li> + <li>Microbat <a href="../cgi-bin/hgTrackUi?db=myoLuc2&g=uniprot" + target=_blank>(myoLuc2)</a></li> + <li>Minke whale <a href="../cgi-bin/hgTrackUi?db=balAcu1&g=uniprot" + target=_blank>(balAcu1)</a></li> + <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=uniprot" + target=_blank>(mm10)</a></li> + <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm9&g=uniprot" + target=_blank>(mm9)</a></li> + <li>Mouse lemur <a href="../cgi-bin/hgTrackUi?db=micMur2&g=uniprot" + target=_blank>(micMur2)</a></li> + <li>Naked mole-rat <a href="../cgi-bin/hgTrackUi?db=hetGla2&g=uniprot" + target=_blank>(hetGla2)</a></li> + <li>Nile tilapia <a href="../cgi-bin/hgTrackUi?db=oreNil2&g=uniprot" + target=_blank>(oreNil2)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Opossum <a href="../cgi-bin/hgTrackUi?db=monDom5&g=uniprot" + target=_blank>(monDom5)</a></li> + <li>Orangutan <a href="../cgi-bin/hgTrackUi?db=ponAbe3&g=uniprot" + target=_blank>(ponAbe3)</a></li> + <li>P. pacificus <a href="../cgi-bin/hgTrackUi?db=priPac1&g=uniprot" + target=_blank>(priPac1)</a></li> + <li>Painted turtle <a href="../cgi-bin/hgTrackUi?db=chrPic1&g=uniprot" + target=_blank>(chrPic1)</a></li> + <li>Panda <a href="../cgi-bin/hgTrackUi?db=ailMel1&g=uniprot" + target=_blank>(ailMel1)</a></li> + <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr3&g=uniprot" + target=_blank>(susScr3)</a></li> + <li>Pika <a href="../cgi-bin/hgTrackUi?db=ochPri3&g=uniprot" + target=_blank>(ochPri3)</a></li> + <li>Platypus <a href="../cgi-bin/hgTrackUi?db=ornAna2&g=uniprot" + target=_blank>(ornAna2)</a></li> + <li>Proboscis monkey <a href="../cgi-bin/hgTrackUi?db=nasLar1&g=uniprot" + target=_blank>(nasLar1)</a></li> + <li>Rabbit <a href="../cgi-bin/hgTrackUi?db=oryCun2&g=uniprot" + target=_blank>(oryCun2)</a></li> + <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn6&g=uniprot" + target=_blank>(rn6)</a></li> + <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac8&g=uniprot" + target=_blank>(rheMac8)</a></li> + <li>Rock hyrax <a href="../cgi-bin/hgTrackUi?db=proCap1&g=uniprot" + target=_blank>(proCap1)</a></li> + <li>S. cerevisiae <a href="../cgi-bin/hgTrackUi?db=sacCer2&g=uniprot" + target=_blank>(sacCer2)</a></li> + <li>S. cerevisiae <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=uniprot" + target=_blank>(sacCer3)</a></li> + <li>S. purpuratus <a href="../cgi-bin/hgTrackUi?db=strPur2&g=uniprot" + target=_blank>(strPur2)</a></li> + <li>SARS-CoV-2 <a href="../cgi-bin/hgTrackUi?db=wuhCor1&g=uniprot" + target=_blank>(wuhCor1)</a></li> + <li>Sea hare <a href="../cgi-bin/hgTrackUi?db=aplCal1&g=uniprot" + target=_blank>(aplCal1)</a></li> + <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri3&g=uniprot" + target=_blank>(oviAri3)</a></li> + <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=uniprot" + target=_blank>(oviAri4)</a></li> + <li>Shrew <a href="../cgi-bin/hgTrackUi?db=sorAra2&g=uniprot" + target=_blank>(sorAra2)</a></li> + <li>Sloth <a href="../cgi-bin/hgTrackUi?db=choHof1&g=uniprot" + target=_blank>(choHof1)</a></li> + <li>Southern sea otter <a href="../cgi-bin/hgTrackUi?db=enhLutNer1&g=uniprot" + target=_blank>(enhLutNer1)</a></li> + <li>Squirrel <a href="../cgi-bin/hgTrackUi?db=speTri2&g=uniprot" + target=_blank>(speTri2)</a></li> + <li>Squirrel monkey <a href="../cgi-bin/hgTrackUi?db=saiBol1&g=uniprot" + target=_blank>(saiBol1)</a></li> + <li>Stickleback <a href="../cgi-bin/hgTrackUi?db=gasAcu1&g=uniprot" + target=_blank>(gasAcu1)</a></li> + <li>Tarsier <a href="../cgi-bin/hgTrackUi?db=tarSyr2&g=uniprot" + target=_blank>(tarSyr2)</a></li> + <li>Tasmanian devil <a href="../cgi-bin/hgTrackUi?db=sarHar1&g=uniprot" + target=_blank>(sarHar1)</a></li> + <li>Tenrec <a href="../cgi-bin/hgTrackUi?db=echTel2&g=uniprot" + target=_blank>(echTel2)</a></li> + <li>Tetraodon <a href="../cgi-bin/hgTrackUi?db=tetNig2&g=uniprot" + target=_blank>(tetNig2)</a></li> + <li>Tibetan frog <a href="../cgi-bin/hgTrackUi?db=nanPar1&g=uniprot" + target=_blank>(nanPar1)</a></li> + <li>Tree shrew <a href="../cgi-bin/hgTrackUi?db=tupBel1&g=uniprot" + target=_blank>(tupBel1)</a></li> + <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=uniprot" + target=_blank>(melGal5)</a></li> + <li>Wallaby <a href="../cgi-bin/hgTrackUi?db=macEug2&g=uniprot" + target=_blank>(macEug2)</a></li> + <li>White rhinoceros <a href="../cgi-bin/hgTrackUi?db=cerSim1&g=uniprot" + target=_blank>(cerSim1)</a></li> + <li>X. tropicalis <a href="../cgi-bin/hgTrackUi?db=xenTro9&g=uniprot" + target=_blank>(xenTro9)</a></li> + <li>Zebra finch <a href="../cgi-bin/hgTrackUi?db=taeGut2&g=uniprot" + target=_blank>(taeGut2)</a></li> + <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer10&g=uniprot" + target=_blank>(danRer10)</a></li> + <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer7&g=uniprot" + target=_blank>(danRer7)</a></li> + </ul></div> +</div></div> +<p> +These tracks will continue to be updated automatically as part of a quarterly pipeline.</p> +<p> +Thanks to UniProt for providing these annotations, as well as +Maximilian Haeussler and Lou Nassar of the UCSC Genome Browser group for their +work in creating and releasing these tracks.</p> + +<a name="111620"></a> +<h2>Nov. 16, 2020 Genome in a Bottle tracks now available for human</h2> +<p> +We are pleased to announce the release of three new tracks from the +<a href="https://www.nist.gov/programs-projects/genome-bottle" target="_blank">Genome in a +Bottle Consortium (GIAB)</a> available for human assemblies, +<a href="../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=giab" target="_blank">GRCh37/hg19</a> and +<a href="../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=giab" target="_blank">GRCh38/hg38</a>. GIAB is an +open, public consortium hosted by <a href="https://www.nist.gov/" target="_blank">NIST</a>. The +priority of GIAB is to develop reference standards, reference methods, and reference data by +authoritative characterization of human genomes for use in benchmarking, including analytical +validation and technology development that will support translation of whole human genome sequencing +to clinical practice. The sole purpose of this work is to provide validated variants and regions to +enable technology and bioinformatics developers to benchmark and optimize their detection methods. +</p> +<p> +There are two phased trio tracks and a structural variants track available: +</p> +<ul> + <li> + <strong>Ashkenazim and the Chinese Trio tracks</strong> - shows benchmark SNV calls from two + son/father/mother trios of Ashkenazi Jewish and Han Chinese ancestry from the Personal Genome + Project, consented for commercial redistribution. + </li> + <li> + <strong>Structural Variants track</strong> - shows benchmark SV calls (nssv) and variant regions + (nsv) (5,262 insertions and 4,095 deletions, > 50 bp, in 2.51 Gb of the genome) from the son + (HG002/NA24385) from the Ashkenazi Jewish trio. + </li> +</ul> +<p> +We would like to thank NCBI, the Genome in a Bottle Consortium, and NIST for providing the +benchmark VCF and BED files. We would also like to thank Chris Lee and Jairo Navarro for the +creation and release of the Genome Browser tracks. +</p> + +<a name="110320"></a> +<h2>Nov. 3, 2020 New gnomAD pext track for Tissue specific transcript expression</h2> +<p> +We are happy to share that we have updated our gnomAD super track to include +the gnomAD pext datasets on the GRCh37/hg19 genome. This track displays isoform +expression levels across 53 tissues based on 11,706 tissue samples from +the Genotype Tissue Expression (GTEx) v7 dataset, showing a comprehensive +view of the expression of exons across +a gene using the proportion expression across transcripts, or pext metric, a +transcript-level annotation metric which quantifies isoform expression for variants. +</p> +<p> +This may be especially useful to those interested in alternative splicing and +clinicial assessment of variants. For more +information, please see the track description page and the associated publication:</p> +<ul> +<li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadPext">Gnomad pext track for hg19 </a></li> +<li><a href="https://www.nature.com/articles/s41586-020-2329-2" target="_blank">Transcript +expression-aware annotation improves rare variant interpretation</a></li> +</ul> +<p> +We would like to thank the gnomAD team at the BROAD institute and the UCSC Genome Browser team members +Chris Lee, Anna Benet-Pages, and Daniel Schmelter for developing, and +releasing this track. +</p> + + <a name="102320"></a> <h2>Oct. 23, 2020 The new GRCm39 Mouse Genome Browser is here</h2> <p> We are pleased to announce the release of a new mouse assembly, mm39, which corresponds to the GRCm39 assembly released by the <a href="https://www.ncbi.nlm.nih.gov/grc/mouse" target="_blank">Genome Reference Consortium</a> (GRC). Starting with this release, the UCSC Genome Browser version numbers for mouse assemblies will match those of the GRC to minimize version confusion. Hence, the GRCm39 assembly is referred to as mm39 in Genome Browser datasets and documentation.</p> <h3>About the assembly (mm39):</h3> <ul> <li> UCSC Genome Browser assembly ID: mm39</li> <li> Sequencing/Assembly provider ID: Genome Reference Consortium Mouse Build 39 (GCA_000001635.9) @@ -396,30 +719,31 @@ <a href="https://www.ncbi.nlm.nih.gov/dbvar/content/overview/" target="_blank">dbVar, the database of Structural Variation from NCBI</a>. The Common Structural Variants track shows variants that meet the following criteria: more than 50 basepairs, occur in at least 100 samples, and have an allele frequency of >=0.01 in at least one population. For more information, please see the track description page:</p> <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=dbVarSv">dbVar Structural Variants </a> (<a href="/cgi-bin/hgTrackUi?db=hg38&g=dbVarSv">hg38</a>/<a href="/cgi-bin/hgTrackUi?db=hg19&g=dbVarSv">hg19</a>)</li> </ul> <p> We thank the dbVar team at NCBI, especially John Lopez and Tim Hefferon for technical coordination and consultation, and to Chris Lee, Anna Benet-Pages, and Daniel Schmelter of the Genome Browser team for developing, and releasing this track. </p> <a name="100120"></a> + <h2>Oct. 1, 2020 New video: Making links to the Genome Browser. Part 3: Composite tracks, custom tracks and spreadsheets </h2> <p> We are happy to announce another release to the UCSC Genome Browser <a href = "https://bit.ly/ucscVideos" target = _blank>YouTube channel</a>. </p> <p> This new video, <a href = "https://bit.ly/ucscVid23" target = _blank>Making links to the UCSC Genome Browser. Part 3: Composite tracks, custom tracks and spreadsheets</a> is the final installment of a three-part series showing how to make links to the Browser. This release features @@ -537,45 +861,45 @@ <h2>Sept. 25, 2020   New data and visualization types: Covid GWAS (Lollypop) and Family Trios (VCF Trios)</h2> <h3>Covid GWAS meta-analysis</h3> <p> We are happy to announce the first COVID-19 tracks in our human genome browsers <a href="../../cgi-bin/hgGateway?db=hg19">GRCh37/hg19</a> and <a href="../../cgi-bin/hgGateway?db=hg38">GRCh38/hg38</a>, the COVID-19 GWAS meta-analysis. This track brings together data from 17 international GWAS studies and aims to identify genetic determinants of SARS-CoV-2 infection susceptibility and disease severity. These data are from the <a href="https://www.covid19hg.org/results/" target="_blank"> COVID-19 Host Genetics Initiative (HGI)</a>, a collaborative effort to analyze and share viral host genetics research. More resources are available on our page: <a href="../../covid19.html">COVID-19 Resources at UCSC</a>. </p> <p> -These data are shown in our new lollypop visualization in order to show the dimensions of +These data are shown in our new lollipop visualization in order to show the dimensions of effect size and p-value in addition to location. Filters are also available for these variables and the number of studies. Custom tracks using the -lollypop format are not yet available. For more information on these +lollipop format are 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/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> <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, +src="../../images/CovidGWAS.png" alt="The COVID-19 GWAS track shows variants as lollipops, 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, Kumar Veerapen, Rachel Liao, and Juha Karjalainen at the Broad Institute for their input during track development. We would also like to thank the UCSC Genome Browser staff Kate Rosenbloom, Daniel Schmelter, Brain Raney, 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