3a884d87e2f5198d79e8c628fad94112ed4d1a01
max
  Mon Feb 15 05:48:31 2021 -0800
updating CADD track docs, refs #18492

diff --git src/hg/makeDb/trackDb/human/caddSuper.html src/hg/makeDb/trackDb/human/caddSuper.html
new file mode 100644
index 0000000..68802e1
--- /dev/null
+++ src/hg/makeDb/trackDb/human/caddSuper.html
@@ -0,0 +1,110 @@
+<h2>Description</h2>
+
+<p> This track collection shows <a href="https://cadd.gs.washington.edu/"
+target="_blank">Combined Annotation Dependent Depletion</a> scores.
+CADD is a tool for scoring the deleteriousness of single nucleotide variants as
+well as insertion/deletions variants in the human genome.</p>
+
+<p>
+Some mutation annotations
+tend to exploit a single information type (e.g. phastCons or phylP for
+conservation) and/or are restricted in scope (e.g. to missense changes). Thus,
+a broadly applicable metric that objectively weights and integrates diverse
+information is needed.  Combined Annotation Dependent Depletion (CADD) is a
+framework that integrates multiple annotations into one metric by contrasting
+variants that survived natural selection with simulated mutations.
+</p>
+
+<p>
+CADD scores strongly correlate with allelic diversity, pathogenicity of both
+coding and non-coding variants, and experimentally measured regulatory effects,
+and also highly rank causal variants within individual genome sequences.
+Finally, CADD scores of complex trait-associated variants from genome-wide
+association studies (GWAS) are significantly higher than matched controls and
+correlate with study sample size, likely reflecting the increased accuracy of
+larger GWAS.
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+<p>
+There are six subtracks of this track: four for every possible single nucleotide mutation, 
+one for insertions and one for deletions. All subtracks show the CADD Phred
+score on mouse over.<p>
+
+<p>
+<b>Single nucleotide variants (SNV):</b> For SNVs, at every
+genome position, there are three values per position, one for every possible
+nucleotide mutation. The fourth value, "no mutation", e.g. A to A, is always
+set to zero.<br>
+When using this track, please zoom in until you can see every basepair at the
+top of the display. Otherwise, there are several nucleotides under your mouse
+cursor per pixel and instead of an actual score, the tooltip text can only show
+the average score of all nucleotides under the cursor, which is indicated by
+the prefix "~" in the mouse over and averages of scores are not useful for any
+application of CADD.
+</p>
+
+<p><b>Insertions and deletions:</b>: Scores are also shown on mouse over for a
+set of insertions and deletions. On hg38, the set has been obtained from
+Gnomad3. On hg19, the set of indels has been obtained from various sources
+(gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest
+is not in the track, you will need to use CADD's
+<a target=_blank href="https://cadd.gs.washington.edu/score">Online scoring tool</a>
+to obtain them.</p>
+
+<H2>Data access</H2>
+<p>
+CADD scores are freely available for all non-commercial applications from <a target=_blank href="https://cadd.gs.washington.edu/download">the CADD website</a>. For commercial applications, see <a target=_blank href="https://cadd.gs.washington.edu/contact">the license instructions</a> there.
+</p>
+
+<p>
+The CADD data on the UCSC Genome Browser can be explored interactively with the
+<a href="../cgi-bin/hgTables">Table Browser</a> or the <a
+href="../cgi-bin/hgIntegrator">Data Integrator</a>.
+For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that
+can be downloaded from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/" target="_blank">our download server</a>.
+The files for this track are called <tt>a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb</tt>. Individual
+regions or the whole genome annotation can be obtained using our tool <tt>bigWigToWig</tt>
+or <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled
+binary for your system. Instructions for downloading source code and binaries can be found
+<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
+The tools
+can also be used to obtain only features within a given range, e.g. <br>
+<tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/a.bw stdout</tt><br>
+or<br>
+<tt>bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/ins.bb stdout</tt></p>
+
+<h2>Methods</h2>
+
+<p>
+Data were converted from the files provided on
+<a href="https://cadd.gs.washington.edu/download" target="_blank">the CADD Downloads website</a>, provided by the Kircher lab,
+using <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/cadd" target=_BLANK>custom Python scripts</a>, 
+documented in our <a target=_BLANK href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/cadd.txt">makeDoc</a> files.
+</p>
+
+<h2>Credits</h2>
+<p>
+Thanks to the CADD development team for providing precomputed data as simple tab-separated files.
+</p>
+
+<h2>References</h2>
+<p>
+Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J.
+<a href="http://dx.doi.org/10.1038/ng.2892" target="_blank">
+    A general framework for estimating the relative pathogenicity of human genetic variants</a>.
+<em>Nat Genet</em>. 2014 Mar;46(3):310-5.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24487276" target="_blank">24487276</a>; PMC: <a
+    href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992975/" target="_blank">PMC3992975</a>
+</p>
+
+<p>
+Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M.
+<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gky1016" target="_blank">
+    CADD: predicting the deleteriousness of variants throughout the human genome</a>.
+<em>Nucleic Acids Res</em>. 2019 Jan 8;47(D1):D886-D894.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30371827" target="_blank">30371827</a>; PMC: <a
+    href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323892/" target="_blank">PMC6323892</a>
+</p>
+