2f53c99dd16cc36dd899b2c237631b30d95d6bbb kate Wed Sep 9 20:44:58 2020 -0700 Clean-up after track, add make doc. refs #26129 diff --git src/hg/makeDb/trackDb/human/covidGwas.html src/hg/makeDb/trackDb/human/covidGwas.html deleted file mode 100644 index 72158c3..0000000 --- src/hg/makeDb/trackDb/human/covidGwas.html +++ /dev/null @@ -1,97 +0,0 @@ -<H2>Description</H2> -<p> -This track set shows <b>GWAS meta-analyses</b> from the -<a target=_blank href="https://www.covid19hg.org/"> -<b>COVID-19 Host Genetics Initiative (HGI)</b></a>, -a collaborative project bringing together the human genetics community to facilitate -the generation, analysis and sharing of COVID-19 host genetics research. -The COVID-19 HGI organizes meta-analyses across multiple studies contributed by -<a target="_blank" href="https://www.covid19hg.org/partners/">partners world-wide</a> -to learn the genetic determinants of SARS-CoV-2 infection susceptibility, disease severity and -outcomes, and provides a platform to share the results from such activities, as well as -the individual-level data where possible. -</p> -<p> -The specific phenotypes studied by the COVID-19 HGI are those that benefit -from maximal sample size. The primary analysis focuses on disease severity. -Two meta-analyses are represented in this track: - -<ul> -<li><b>ANA_C2_V2</b>: covid vs. population (6696 cases from 18 studies)</li> -<li><b>ANA_B2_V2</b>: hospitalized covid vs. population (3199 cases from 8 studies)</li> -</ul> - -<H2>Display Conventions</H2> -<p> -Displayed items are colored by <b>GWAS effect</b>: red for positive, blue for negative. -The height of the item reflects the <b>effect size</b> (log OR scale). -The color saturation indicates <b>statistical significance</b>: greater than .05 pValue are -brightly colored (bright red -<span style='background-color: #ff0000;'> </span> -, bright blue -<span style='background-color: #0000ff;'> </span> -), -those with less significance are paler (light red -<span style='background-color: #ffa0a0;'> </span> -, light blue -<span style='background-color: #a0a0ff;'> </span> -). -</p> - -<p> -Each track has separate display controls and data can be filtered according to the -<b>number of studies</b>, <b>minimum -log10 p-value</b>, and the -<b>effect size on log(OR) scale</b>, using the track <b>Configure</b> options. -</p> - -<p> -<b>Mouseover</b> on items shows the rs ID (or chrom:pos if none assigned), both the non-effect -and effect alleles, -the effect size on log(OR) scale, the -log10 p-value, and the number of studies. -Further information on each variant is displayed on the details page by a click onto any item. -</p> - -<H2>Methods</H2> -<p> -Data was generated from genome wide SNP array, exome and genome sequencing, leveraging the impact -of both common and rare variants. Statistical analysis takes into account differences between -sexes, ancestries, and date of sample collection. More information about the prospective studies, -processing pipeline, results and data sharing can be found -<a target=_blank href="https://www.covid19hg.org/about/">here</a>. -</p> - - -<H2>Data Access</H2> -<p> -The data underlying these tracks and summary statistics results are publicly available in -<a target=_blank href="https://www.covid19hg.org/results">COVID19-hg Release 3 (June 2020)</a>. -The raw data can be explored interactively with the <a target="_blank" href="../cgi-bin/hgTables"> -Table Browser</a>, or the <a target="_blank" href="../cgi-bin/hgIntegrator">Data Integrator</a>. -For automated analysis, the data may be queried from our <a target="_blank" -href="/goldenPath/help/api.html">REST API</a>. Please refer to -our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" -target="_blank">mailing list archives</a> for questions, or our <a target="_blank" -href="../FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more information. -</p> - -<H2>Credits</H2> -<p> -Thanks to the COVID-19 Host Genetics Initiative contributors and project leads for making these -data available, and in particular to Rachel Liao and Juha Karjalainen at the Broad Institute for -their review and input during browser track development. -</p> - -<H2>References</H2> - -<p> -COVID-19 Host Genetics Initiative. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/32404885" target="_blank"> -The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic -factors in susceptibility and severity of the SARS-CoV-2 virus pandemic</a>. -<em>Eur J Hum Genet</em>. 2020 Jun;28(6):715-718. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32404885" target="_blank">32404885</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7220587/" target="_blank">PMC7220587</a> -</p> - - -