fbe00baffdd77e3280b684b54757de7090cf21e9 gperez2 Tue Dec 16 16:37:41 2025 -0800 Updating the EVA SNP track description, adding pennantIcon, and adding beta tag, refs #36512 diff --git src/hg/makeDb/trackDb/evaSnpContainer.html src/hg/makeDb/trackDb/evaSnpContainer.html index 9cb55a93e0c..fefdcafaadb 100644 --- src/hg/makeDb/trackDb/evaSnpContainer.html +++ src/hg/makeDb/trackDb/evaSnpContainer.html @@ -33,35 +33,35 @@ class of the variant as reported by EVA, the source of the data, the amino acid change, if any, and the functional class as determined by UCSC's Variant Annotation Integrator. </p> <p>Variants can be filtered using the track controls to show subsets of the data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or by color, which bins the UCSC functional effects into general classes.</p> <h3>Mouse-over</h3> <p> Mousing over an item shows the ucscClass, which is the consequence according to the <a target="_blank" href="/cgi-bin/hgVai">Variant Annotation Integrator</a>, and the aaChange when one is available, which is the change in amino acid in HGVS.p terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over -in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID -separated by spaces describing all possible AA changes.</p> +in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID, +separated by spaces, describing all possible AA changes.</p> <p> Multiple items may appear due to different variant predictions on multiple gene transcripts. -For all organisms, the gene models used were the NCBI RefSeq curated when available, if not then +For all organisms, the gene models used were the NCBI RefSeq curated when available, if not, then ensembl genes, or finally, UCSC mappings of RefSeq if neither of the previous models was possible. </p> <h3>Track colors</h3> <p> Variants are colored according to the most potentially deleterious functional effect prediction according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section below. </p> <p> <table cellpadding='2'> <thead><tr> <th style="border-bottom: 2px solid;">Color</th> @@ -75,134 +75,134 @@ </p> <h3>Sequence Ontology (SO)</h3> <p> Variants are classified by EVA into one of the following <a target="_blank" href="http://www.sequenceontology.org/">sequence ontology</a> terms: </p> <ul> <li> <b>substitution</b> — A single nucleotide in the reference is replaced by another, alternate allele. <li> <b>deletion</b> — One or more nucleotides are deleted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the - Alternate Allele field (Alt). E.g. a variant that is a deletion of an A - maybe be represented as Ref = GA and Alt = G. + Alternate Allele field (Alt). E.g., a variant that is a deletion of an A + may be represented as Ref = GA and Alt = G. <li> <b>insertion</b> — One or more nucleotides are inserted. The representation in the database is to display one additional nucleotide in both the Reference field (Ref) and the - Alternate Allele field (Alt). E.g. a variant that is an insertion of a T may + Alternate Allele field (Alt). E.g., a variant that is an insertion of a T may be represented as Ref = G and Alt = GT. <li> <b>delins</b> — Similar to a tandem repeat, in that the runs of Ref and Alt Alleles are of different length, except that there is more than one type of nucleotide, e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. <li> <b>multipleNucleotideVariant</b> — More than one nucleotide is substituted by an equal number of different nucleotides, e.g., Ref = AA, Alt = GC. <li> <b>sequence alteration</b> — A parent term meant to signify a deviation from another sequence. Can be assigned to variants that have not been characterized yet. </ul> </p> <h2>Methods</h2> <p> Data were downloaded from the European Variation Archive EVA <a href="https://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/" target="_blank">current_ids.vcf.gz</a> files corresponding to the proper assembly.</p> <p> -Chromosome names were converted to UCSC-style -and the variants passed through the +Chromosome names were converted to UCSC-style, +and the variants were passed through the <a target="_blank" href="/cgi-bin/hgVai">Variant Annotation Integrator</a> to -predict consequence. For every organism the NCBI RefSeq curated models were used when available, +predict consequence. For every organism, the NCBI RefSeq curated models were used when available, followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models were possible.</p> <p> Variants were then colored according to their predicted consequence in the following fashion: <ul> <li><b><font color=red>Protein-altering variants</font></b> and <b><font color=red> splice site variants</font></b> - exon_loss_variant, frameshift_variant, inframe_deletion, inframe_insertion, initiator_codon_variant, missense_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, stop_gained, stop_lost, coding_sequence_variant, transcript_ablation</li> <li><b><font color=green>Synonymous codon variants</font></b> - synonymous_variant, stop_retained_variant</li> <li><b><font color=blue>Non-coding transcript </font></b> or <b><font color=blue>Untranslated Region (UTR) variants</font></b> - 5_prime_UTR_variant, 3_prime_UTR_variant, complex_transcript_variant, non_coding_transcript_exon_variant</li> <li><b>Intergenic and intronic variants</b> - upstream_gene_variant, downstream_gene_variant, intron_variant, intergenic_variant, NMD_transcript_variant, no_sequence_alteration</li></ul> </p> <p> Sequence Ontology ("<a href="http://www.sequenceontology.org/browser/current_release" target="_blank">SO</a>:") terms were converted to the variant classes, then the files were converted to BED, -and then bigBed format. +and then to 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. +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/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>, +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 +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/$db/bbi/" target="_blank">our download server</a>. Use the corresponding version number for the track -of interest, e.g. <tt>evaSnp8.bb</tt>. +of interest, e.g., <tt>evaSnp8.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool -<tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled +<tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, e.g. <br><br> <tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/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. +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. <a href="https://doi.org/10.1093/nar/gkab960" target="_blank">doi:10.1093/nar/gkab960</a>. Epub ahead of print. PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/34718739/" target="_blank">34718739</a>. PMID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/pmc8728205/" target="_blank">PMC8728205</a>. </p> <p> Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS,