dc28e7eaba410716bba6a5f86c78a11b9e817a61 dschmelt Mon Oct 5 15:04:15 2020 -0700 Small link fixes for dbVar refs #25423 diff --git src/hg/makeDb/trackDb/human/dbVarCurated.html src/hg/makeDb/trackDb/human/dbVarCurated.html index b7e94ca..c34af44 100644 --- src/hg/makeDb/trackDb/human/dbVarCurated.html +++ src/hg/makeDb/trackDb/human/dbVarCurated.html @@ -18,69 +18,78 @@ <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"> +<li><a href="/cgi-bin/hgTrackUi?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"> +<li><a href="/cgi-bin/hgTrackUi?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 +<a href="../../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, +<a href="hgTables">Table Browser</a>, or the +<a href="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>, 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>. +<a href="../../goldenPath/help/api.html">REST API</a>. +<p>The data can also be found directly from the <a target=_blank +href="https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/#data_access">dbVar +nstd186 data access</a>, as well as in the +<a href="hgHubConnect?hubUrl= +https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt&hgHub_do_redirect=on"> +dbVar Track Hub</a>, where additional subtracks are included. For questions about +dbVar track data, please contact <A HREF="mailto:dbvar@ncbi. +nlm. +nih. +gov"> +dbvar@ncbi. +nlm. +nih. +gov</A>. +<!-- above address is dbvar at ncbi.nlm.nih.gov --> </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. +</p> <h2>Credits</h2> <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.