Insertions and deletions:: Scores are also shown on mouseover 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 Online scoring tool to obtain them.
-CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. +CADD scores are freely available for all non-commercial applications from +the CADD website. For commercial +applications, see the license +instructions there.
The CADD 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 and bigBed files that
-can be downloaded from
+Table Browser or the
+Data Integrator.
+For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed
+files that can be downloaded from
our download server.
The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual
regions or the whole genome annotation can be obtained using our tool bigWigToWig
or bigBedToBed 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 only features within a given range, e.g.
-bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/a.bw stdout
-or
+The tools can also be used to obtain only features within a given range, e.g.
+
+bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/a.bw stdout
+
+or
+
bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/ins.bb stdout
Data were converted from the files provided on -the CADD Downloads website, provided by the Kircher lab, -using custom Python scripts, -documented in our makeDoc files. +the CADD Downloads website, +provided by the Kircher lab, using custom Python scripts, +documented in our +makeDoc files.
Thanks to the CADD development team for providing precomputed data as simple tab-separated files.
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. -PMID: 24487276; PMC: PMC3992975 +PMID: 24487276; +PMC: PMC3992975
Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. -PMID: 30371827; PMC: PMC6323892 +PMID: 30371827; +PMC: PMC6323892
-