40710f848501eb48692babdc889a513f3dcda7ef abenetpa Fri Sep 25 09:01:51 2020 -0700 improved color code descriptions refs #25424 diff --git src/hg/makeDb/trackDb/human/dbVarCommon.html src/hg/makeDb/trackDb/human/dbVarCommon.html index a386a35..f619a9a 100644 --- src/hg/makeDb/trackDb/human/dbVarCommon.html +++ src/hg/makeDb/trackDb/human/dbVarCommon.html @@ -43,42 +43,49 @@ <a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186">Variants</a> with AF >= 0.01 for Global Population.</li> <li><b>NCBI Curated Common SVs: all populations from gnomAD - </b> <a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186">Variants</a> with AF >= 0.01 from gnomAD Structural Variants.</li> <li><b>NCBI Curated Common SVs: all populations from 1000 Genomes - </b> <a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186">Variants</a> with AF >= 0.01 from 1000 Genomes Consortium Phase 3 Integrated SV.</li> <li><b>NCBI Curated Common SVs: all populations from DECIPHER -</b> <a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186">Variants</a> with AF >= 0.01 from DECIPHER Consensus CNVs.</li> </ul> </p> <h2>Display Conventions and Configuration</h2> -Items in all subtracks follow the same conventions: items are shaded according to variant type. +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. Mouseover on items indicates -Allele Frequencies (AF). All tracks can be filtered according to the Variant Size and Variant Type. +<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 Size</b> and <b>Variant Type</b>. +</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, 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 +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>. </p> <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> <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>.