7dc8844af53ddba9a7a62a84e94ad8d5f695c374 abenetpa Fri Oct 2 14:53:56 2020 -0700 added john lopez to credits and dbVar hub data access #25424 diff --git src/hg/makeDb/trackDb/human/dbVarCurated.html src/hg/makeDb/trackDb/human/dbVarCurated.html index 29c956c..b7e94ca 100644 --- src/hg/makeDb/trackDb/human/dbVarCurated.html +++ src/hg/makeDb/trackDb/human/dbVarCurated.html @@ -1,85 +1,90 @@ <h2>Description</h2> <p> The tracks listed here contain data from the <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/content/var_summary/#nstd186"> nstd186 (NCBI Curated Common Structural Variants)</a> study. This is a collection of structural variants (SV) originally submitted to dbVar which are part of a study with at least 100 samples and have an allele frequency of >=0.01 in at least one population. The complete dataset is imported from these common-population studies: </p> <p> <b>gnomAD Structural Variants</b> <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd166/">(nstd166)</a>: Catalog of SVs detected from the sequencing of the complete genome of 10,847 unrelated individuals from the GnomAD v2.1 release.</p> <p> <b>1000 Genomes Consortium Phase 3 Integrated SV</b> <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/estd219/">(estd219)</a>: Structural variants of the 1000 Genomes project Phase 3 as reported in a separate article specifically dedicated to the analysis of SVs. Many of these data are identical to those reported in the <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/estd214/">estd214</a> study.</p> <p> <b>DECIPHER Common CNVs</b> <a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd183/">(nstd183)</a>: Consensus set of common population CNVs selected from high-resolution controls sets where frequency information is available. </p> <p> There are two tracks in this collection: <ul> <li><a href="/cgi-bin/hgTrackUi?hgsid=395092309_WCeXo2V0Ug6yJ1KducDbjPkMSade&c=chr1&g=dbVar_common"> <b>NCBI dbVar Curated Common Structural Variants (dbVar Common SV)</b></a>: Shows copy number variants calls (variants >=50 nucleotides) from the <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186/">nstd186</a> study.</li> <li><a href="/cgi-bin/hgTrackUi?hgsid=395092309_WCeXo2V0Ug6yJ1KducDbjPkMSade&c=chr1&g=dbVar_conflict"> <b>NCBI dbVar Curated Conflict Variants (dbVar Conflict SV)</b></a>: Shows copy number variants from <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186/">nstd186</a> (NCBI Curated Common Structural Variants) that overlap with <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd102/">nstd102</a> (Clinical Structural Variants).</li> </ul> </p> <h2>Display Conventions</h2> <p> These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described <a href="https://genome.ucsc.edu/goldenPath/help/multiView.html">here</a>. Some dbVar tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. </p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a href="https://genome.ucsc.edu/cgi-bin/hgTables">Table Browser</a>, or the <a href="https://genome.ucsc.edu/cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a href="https://genome.ucsc.edu/goldenPath/help/api.html">REST API</a>. The data can also be found directly from the dbVar nstd186 <a target=_blank -href="https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/#data_access">data access</a>. -For questions about dbVar track data, please contact <em>dbvar@ncbi.nlm.nih.gov</em>. +href="https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/#data_access">data access</a>, as +well as in the <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect?hgsid=910263067_X3tU6DiJPhKMr71o1h9Zj2K5XQ4u" +>dbVar Track Hub</a>, where additional subtracks are included. For questions about dbVar track +data, please contact <em>dbvar@ncbi.nlm.nih.gov</em>. </p> +<p> +The data can also be found directly from the dbVar nstd186 data access, as well as in the dbVar Track Hub [https://genome.ucsc.edu/cgi-bin/hgHubConnect?hgsid=910263067_X3tU6DiJPhKMr71o1h9Zj2K5XQ4u], where additional subtracks are included. For questions about dbVar track data, please contact dbvar@ncbi.nlm.nih.gov. + <h2>Credits</h2> <p> -Thanks to the dbVAR team at NCBI, especially Timothy Hefferon for technical coordination and -consultation, and to Christopher Lee, Anna Benet-Pages, and Maximilian Haeussler of the Genome -Browser team for engineering the track display.</p> +Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical +coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter of +the Genome Browser team for engineering the track display.</p> <h2>References</h2> <p> Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G <em>et al</em>. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gks1213" target="_blank"> DbVar and DGVa: public archives for genomic structural variation</a>. <em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D936-41. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193291" target="_blank">23193291</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531204/" target="_blank">PMC3531204</a> </p>