04282647de9c5688da55b7c2debc412d92a7c3d7 jnavarr5 Thu Feb 25 14:48:29 2021 -0800 Making each line less than 100 characters, refs #18492 diff --git src/hg/makeDb/trackDb/human/caddSuper.html src/hg/makeDb/trackDb/human/caddSuper.html index cbc05cc..71e8baf 100644 --- src/hg/makeDb/trackDb/human/caddSuper.html +++ src/hg/makeDb/trackDb/human/caddSuper.html @@ -42,69 +42,74 @@ 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. </p> <p><b>Insertions and deletions:</b>: 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 <a target=_blank href="https://cadd.gs.washington.edu/score">Online scoring tool</a> to obtain them.</p> <H2>Data access</H2> <p> -CADD scores are freely available for all non-commercial applications from <a target=_blank href="https://cadd.gs.washington.edu/download">the CADD website</a>. For commercial applications, see <a target=_blank href="https://cadd.gs.washington.edu/contact">the license instructions</a> there. +CADD scores are freely available for all non-commercial applications from +<a target=_blank href="https://cadd.gs.washington.edu/download">the CADD website</a>. For commercial +applications, see <a target=_blank href="https://cadd.gs.washington.edu/contact">the license +instructions</a> there. </p> <p> The CADD 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 and bigBed files that -can be downloaded from +<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 and bigBed +files that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/" target="_blank">our download server</a>. The files for this track are called <tt>a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigWigToWig</tt> or <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. -The tools -can also be used to obtain only features within a given range, e.g. <br> -<tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/a.bw stdout</tt><br> -or<br> +The tools can also be used to obtain only features within a given range, e.g. +<br> +<tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/a.bw stdout</tt> +<br> +or +<br> <tt>bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/cadd/ins.bb stdout</tt></p> <h2>Methods</h2> <p> Data were converted from the files provided on -<a href="https://cadd.gs.washington.edu/download" target="_blank">the CADD Downloads website</a>, provided by the Kircher lab, -using <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/cadd" target=_BLANK>custom Python scripts</a>, -documented in our <a target=_BLANK href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/cadd.txt">makeDoc</a> files. +<a href="https://cadd.gs.washington.edu/download" target="_blank">the CADD Downloads website</a>, +provided by the Kircher lab, using <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/cadd" target=_BLANK>custom Python scripts</a>, +documented in our +<a target=_BLANK href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/cadd.txt">makeDoc</a> files. </p> <h2>Credits</h2> <p> Thanks to the CADD development team for providing precomputed data as simple tab-separated files. </p> <h2>References</h2> <p> Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. <a href="http://dx.doi.org/10.1038/ng.2892" target="_blank"> A general framework for estimating the relative pathogenicity of human genetic variants</a>. <em>Nat Genet</em>. 2014 Mar;46(3):310-5. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24487276" target="_blank">24487276</a>; PMC: <a - href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992975/" target="_blank">PMC3992975</a> +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24487276" target="_blank">24487276</a>; +PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992975/" target="_blank">PMC3992975</a> </p> <p> Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gky1016" target="_blank"> CADD: predicting the deleteriousness of variants throughout the human genome</a>. <em>Nucleic Acids Res</em>. 2019 Jan 8;47(D1):D886-D894. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30371827" target="_blank">30371827</a>; PMC: <a - href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323892/" target="_blank">PMC6323892</a> +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30371827" target="_blank">30371827</a>; +PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323892/" target="_blank">PMC6323892</a> </p> -