3e1960b35a07377b46bd83b8fd04387f182c6bd6 abenetpa Fri May 15 10:52:51 2020 -0700 added three description pages for dbVar tracks refs #25424 diff --git src/hg/makeDb/trackDb/human/dbVarCommon.html src/hg/makeDb/trackDb/human/dbVarCommon.html new file mode 100644 index 0000000..d2f88c4 --- /dev/null +++ src/hg/makeDb/trackDb/human/dbVarCommon.html @@ -0,0 +1,92 @@ + <h2>Description</h2> + +<p> +This track displays common copy number genomic variations from <a target=_blank +href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186/">nstd186 (NCBI Curated Common +Structural Variants)</a>, divided into subtracks according to population and source of original +submission. +</p> + +<p> +This curated dataset of all structural variants in dbVar includes variants from <b>gnomAD</b>, <b>1000 +Genomes Phase 3</b>, and <b>DECIPHER</b> (dbVar studies +<a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd166/">nstd166</a>, +<a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/estd219/">estd219</a>, and +<a target=_blank href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd183/">nstd183</a>, respectively). +</p> + +<p> +It only includes copy number gain, copy number loss, copy number variation, duplications, and +deletions (including mobile element deletions), that are part of a study with at least 100 samples, +include allele frequency data, and have an allele frequency of >=0.01 in at least one population. +</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> + +<p> +There are six subtracks in this track set: +</p> + +<p> +<ul> +<li><b>NCBI Curated Common SVs: African -</b> +<a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186">Variants</a> with AF >= 0.01 for +African Population.</li> +<li><b>NCBI Curated Common SVs: European -</b> +<a href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd186">Variants</a> with AF >= 0.01 for +European Population.</li> +<li><b>NCBI Curated Common SVs: all populations -</b> +<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. +<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. + +<h2>Data Acces</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 +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 Genom +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> + +