This track collection shows Rare Exome Variant Ensemble Learner (REVEL) scores for predicting +the deleteriousness of each nucleotide change in the genome. +
+ ++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. +
+ ++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. +
+ +
+Single nucleotide variants (SNV): 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.
+
+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.
+
+REVEL scores are available at the + +REVEL website. +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. + +
+ +
+The REVEL data on the UCSC Genome Browser can be explored interactively with the
+Table Browser or the
+Data Integrator.
+For automated download and analysis, the genome annotation is stored at UCSC in bigWig
+files that can be downloaded from
+our download server.
+The files for this track are called a.bw, c.bw, g.bw, t.bw. Individual
+regions or the whole genome annotation can be obtained using our tool bigWigToWig
+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
+here.
+The tools can also be used to obtain features confined to given range, e.g.
+
+
+bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/revel/a.bw stdout
+
+
+
+Data were converted from the files provided on +the REVEL Downloads website. +
+ ++Thanks to the REVEL development team for providing precomputed data. +
+ ++Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, +Musolf A, Li Q, Holzinger E, Karyadi D, et al. + +REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants +Am J Hum Genet. 2016 Oct 6;99(4):877-885. +PMID: 27666373; +PMC: PMC5065685 +
+