dc28e7eaba410716bba6a5f86c78a11b9e817a61 dschmelt Mon Oct 5 15:04:15 2020 -0700 Small link fixes for dbVar refs #25423 diff --git src/hg/makeDb/trackDb/human/dbVarConflict.html src/hg/makeDb/trackDb/human/dbVarConflict.html index d2c005d..d509497 100644 --- src/hg/makeDb/trackDb/human/dbVarConflict.html +++ src/hg/makeDb/trackDb/human/dbVarConflict.html @@ -1,71 +1,82 @@ <h2>Description</h2> The track <b>NCBI dbVar Curated Common SVs: Conflicts with Pathogenic</b> highlights loci where common copy number variants from <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186/">nstd186 (NCBI Curated Common Structural Variants)</a> overlap with structural Variants with clinical assertions, submitted to ClinVar by external labs <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/content/var_summary/#nstd102">(Clinical Structural Variants - nstd102)</a>. </p> <p> <em>Overlap</em> in the track refers to reciprocal overlap between variants in the <b><em>common</em> (NCBI Curated Common Structural Variants)</b> versus <b><em>clinical</em> (ClinVar Long Variants)</b> tracks. Reciprocal overlap values can be anywhere from 10% to 100%. </p> <p> For more information on the number of variant calls and latest statistics for nstd186 see <a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/content/common_summary/">Summary of nstd186</a> (NCBI Curated Common Structural Variants). </p> <h2>Display Conventions and Configuration</h2> <p> Items in all subtracks follow the same conventions: items are colored by variant type, and are based on the dbVar colors described in the <a target="_blank" href="https://www.ncbi.nlm.nih.gov/dbvar/content/overview/">dbVar Overview page</a>. <b><font color="red">Red</font></b> for copy number loss or deletion, <b><font color="blue">blue</font></b> for copy number gain or duplication, and <b><font color="#662180">violet</font></b> for copy number variation. </p> <p> <b>Mouseover</b> on items indicates genes affected, size, variant type, and allele frequencies (AF). All tracks can be filtered according to the <b>variant length</b>, <b>variant type</b> and <b>variant overlap</b>. This last filter defines four bins within that range from which the user can choose. </p> <h2>Data Access</h2> 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> + +<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> -<h2>Credits</h2> 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>