bab72b3c808c25df14fb563dc33336ff79a1f629 kuhn Tue Apr 26 15:14:18 2022 -0700 moved canFam3 evaSnp track to top level for consistency with Lous pipeline. combined html page to include some extra info that was in the canFam3 page diff --git src/hg/makeDb/trackDb/evaSnp.html src/hg/makeDb/trackDb/evaSnp.html index fc77b53..90ca20b 100644 --- src/hg/makeDb/trackDb/evaSnp.html +++ src/hg/makeDb/trackDb/evaSnp.html @@ -103,59 +103,67 @@ 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 release 3 (2022-02-24) <a href="https://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_3/by_assembly/" target="_blank">current_ids.vcf.gz</a> files corresponding to the proper assembly.</p> <p> Chromosome names were converted to UCSC-style, a few problematic variants were removed, and the variants passed through the -<a target="_blank" href="/cgi-bin/hgVai">Variant Annotation Integrator</a> in order to +<a target="_blank" href="/cgi-bin/hgVai">Variant Annotation Integrator</a> to predict consequence. For every organism the ncbiRefSeqCurated gene models were used to predict the consequences, except for mm39 which used the ncbiRefSeqSelect models.</p> <p> Variants were then colored according to their predicted consequence in the following fashion: <ul> -<li><b><font color=red>Protein-altering variants and splice site variants</font></b> +<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 or Untranslated Region (UTR) variants</font></b> +<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. </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 persepective the genomic sequence. For complete documentation of the processing of these tracks, read the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/evaSnp3.txt"> EVA Release 3 MakeDoc</a>.</p> <h2>Data Access</h2> <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