8afa5f78425ec225b329db5e1e204384ad0bdfc1 max Tue Jun 1 05:06:00 2021 -0700 adding revel track for hg38, refs #27142 diff --git src/hg/makeDb/trackDb/human/revel.html src/hg/makeDb/trackDb/human/revel.html index 08ec086..df7d611 100644 --- src/hg/makeDb/trackDb/human/revel.html +++ src/hg/makeDb/trackDb/human/revel.html @@ -14,81 +14,92 @@ 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 +For single nucleotide variants (SNV), 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. +your mouse cursor and no score will be shown on the mouseover tooltip. +</p> + +<p>For hg38, note that the data was converted from the hg19 data using the UCSC +liftOver program, by the REVEL authors. This can lead to missing values or +duplicated values. When a hg38 position is annotated with two scores due to the +lifting, the authors removed all the scores for this position. They did the same when +due to a reference change a mutation in hg19 is not a mutation in hg38 anymore, but the +reference nucleotide. Also, on hg38, the track has the "lifted" icon to indicate +this. You can double-check if a nucleotide +position is possibly affected by the lifting procedure by activating the track +"Hg19 Mapping" under "Mapping and Sequencing". </p> <h2>Data access</h2> <p> REVEL scores are available at the -<a href="https://sites.google.com/site/revelgenomics/ target="_blank"> +<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 among 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>. +target = "_blank">the REVEL Downloads website</a>. As with all other tracks, +a full log of all commands used for the conversion is available in our +<a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/">source repository</a>, for <a target=_blank href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg19.txt">hg19</a> and <a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/revel.txt">hg38</a>. The release used for each assembly is shown on the track description page. + </p> <h2>Credits</h2> <p> -Thanks to the REVEL development team for providing precomputed data. +Thanks to the REVEL development team for providing precomputed data and fixing duplicated values in the hg38 files. </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>