7e0aebd06b2394517d4700aaba6e79ec522a4734 lrnassar Mon Oct 20 15:46:55 2025 -0700 Staging evaSnp8 and one change from ENCODE 4 cCREs I also had stages, refs #36512 #34923 diff --git src/hg/makeDb/trackDb/evaSnpContainer.html src/hg/makeDb/trackDb/evaSnpContainer.html index c9db5f626d1..9cb55a93e0c 100644 --- src/hg/makeDb/trackDb/evaSnpContainer.html +++ src/hg/makeDb/trackDb/evaSnpContainer.html @@ -144,58 +144,58 @@ terms were converted to the variant classes, then the files were converted to BED, and then bigBed format. </p> <p> No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). Amino-acid substitutions for missense variants are based on RefSeq alignments of mRNA transcripts, which do not always match the amino acids predicted from translating the genomic sequence. Therefore, in some instances, the variant and the genomic nucleotide and associated amino acid may be reversed. E.g., a Pro > Arg change from the perspective of the mRNA would be Arg > Pro from the perspective of the genomic sequence. Also, in bosTau9, galGal5, rheMac10, and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. For complete documentation of the processing of these tracks, see the makedoc corresponding to the version of interest. For example, the -<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/evaSnp7.txt"> -EVA Release 7 MakeDoc</a>.</p> +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/evaSnp8.txt"> +EVA Release 8 MakeDoc</a>.</p> <h2>Data Access</h2> <p> <b>Note:</b> It is not recommended to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following <a href="/FAQ/FAQreleases.html#snpConversion">FAQ entry</a>.</p> <p> The data 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 analysis, the data may be queried from our <a href="/goldenPath/help/api.html">REST API</a>. Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a> for questions, or our <a href="/FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more information.</p> <p> For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from <a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/" target="_blank">our download server</a>. Use the corresponding version number for the track -of interest, e.g. <tt>evaSnp7.bb</tt>. +of interest, e.g. <tt>evaSnp8.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, e.g. <br><br> -<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/evaSnp7.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt> +<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/evaSnp8.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt> </p> <h2>Credits</h2> <p> This track was produced from the <a target="_blank" href="https://www.ebi.ac.uk/eva/">European Variation Archive release</a> data. Consequences were predicted using UCSC's Variant Annotation Integrator and NCBI's RefSeq as well as ensembl gene models. </p> <h2>References</h2> <p> Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S <em>et al.</em> <a href="https://doi.org/10.1093/nar/gkab960" target="_blank">The European Variation Archive: a FAIR resource of genomic variation for all species</a>. <em>Nucleic Acids Res.</em> 2021 Oct 28:gkab960.