64868846b5a38ce13f3c5bce12bc97b5d85d5424 kuhn Fri May 21 11:26:37 2021 -0700 made track description for revel and some changes to description for the cadd tracks diff --git src/hg/makeDb/trackDb/human/revel.html src/hg/makeDb/trackDb/human/revel.html new file mode 100644 index 0000000..a5fe200 --- /dev/null +++ src/hg/makeDb/trackDb/human/revel.html @@ -0,0 +1,94 @@ +<h2>Description</h2> + +<p> This track collection shows <a href="https://sites.google.com/site/revelgenomics/" +target="_blank">Rare Exome Variant Ensemble Learner</a> (REVEL) scores for predicting +the deleteriousness of each nucleotide change in the genome. +</p> + +<p> +REVEL is an ensemble method for predicting the pathogenicity of missense variants +based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, +VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, +SiPhy, phyloP, and phastCons. REVEL was trained using recently discovered pathogenic +and rare neutral missense variants, excluding those previously used to train its +constituent tools. The REVEL score for an individual missense variant can range +from 0 to 1, with higher scores reflecting greater likelihood that the variant is +disease-causing. +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +There are four subtracks for this track: one for every nucleotide showing +a score for the mutation represented by a mutation from the reference to that +nucleotide. All subtracks show the REVEL ensemble score on mouseover, representing +each of the possible ~9 billion SNVs in the genome. The score is an aggregation +of the outputs of the 13 tools. +</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", representing +the reference allele, e.g. A to A, is always set to zero. +<br> +When using this track, zoom in until you can see every basepair at the +top of the display. Otherwise, there are several nucleotides per pixel under +your mouse cursor and instead of an actual score, the tooltip text will show +the average score of all nucleotides under the cursor. This is indicated by +the prefix "~" in the mouseover. Averages of scores are not useful for any +application of REVEL. +</p> + +<h2>Data access</h2> +<p> +REVEL scores are available at the +<a href="https://sites.google.com/site/revelgenomics/ target="_blank"> +REVEL website</a>. +The site provides precomputed REVEL scores for all possible human missense variants +to facilitate the identification of pathogenic variants amoung the large number of +rare variants discovered in sequencing studies. + +</p> + +<p> +The REVEL 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 +files that can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/revel/" target="_blank">our download server</a>. +The files for this track are called <tt>a.bw, c.bw, g.bw, t.bw</tt>. Individual +regions or the whole genome annotation can be obtained using our tool <tt>bigWigToWig</tt> +which can be compiled from the source code or downloaded as a precompiled +binary for your system. Instructions for downloading source code and binaries can be found +<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. +The tools can also be used to obtain features confined to given range, e.g. +<br> +<br> +<tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/revel/a.bw stdout</tt> +<br> + +<h2>Methods</h2> + +<p> +Data were converted from the files provided on +<a href="https://sites.google.com/site/revelgenomics/downloads?authuser=0" +target = "_blank">the REVEL Downloads website</a>. +</p> + +<h2>Credits</h2> +<p> +Thanks to the REVEL development team for providing precomputed data. +</p> + +<h2>References</h2> +<p> +Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, +Musolf A, Li Q, Holzinger E, Karyadi D, et al. +<a href="https://doi.org/10.1016/j.ajhg.2016.08.016" target = _blank"> +REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants</a> +<em>Am J Hum Genet</em>. 2016 Oct 6;99(4):877-885. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27666373" target="_blank">27666373</a>; +PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065685/" target="_blank">PMC5065685</a> +</p> +