00d7ec5697fe5ff72b7d6a2a907bd4384fd0b9aa jnavarr5 Thu Feb 25 14:56:48 2021 -0800 Adding double quotes around _blank attribute. Making 'Online' lowercase. Making

tag lowercase, refs #18492 diff --git src/hg/makeDb/trackDb/human/caddSuper.html src/hg/makeDb/trackDb/human/caddSuper.html index 71e8baf..9554d13 100644 --- src/hg/makeDb/trackDb/human/caddSuper.html +++ src/hg/makeDb/trackDb/human/caddSuper.html @@ -37,69 +37,72 @@ nucleotide mutation. The fourth value, "no mutation", e.g. A to A, is always set to zero.
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 mouseover and averages of scores are not useful for any application of CADD.

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 +online scoring tool to obtain them.

-

Data access

+

Data access

CADD scores are freely available for all non-commercial applications from -the CADD website. For commercial -applications, see the license -instructions there. +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 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/$db/cadd/a.bw stdout
or
bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/ins.bb stdout

Methods

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. +provided by the Kircher lab, using + +custom Python scripts, +documented in our +makeDoc files.

Credits

Thanks to the CADD development team for providing precomputed data as simple tab-separated files.

References

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