73a60632e0f247a57d5755ec8080db20f342ef34 abenetpa Wed Sep 2 00:35:07 2020 -0700 corrected typos in clinvar.html refs #26147 diff --git src/hg/makeDb/trackDb/human/clinvar.html src/hg/makeDb/trackDb/human/clinvar.html index 3adf238..a7f3661 100644 --- src/hg/makeDb/trackDb/human/clinvar.html +++ src/hg/makeDb/trackDb/human/clinvar.html @@ -11,58 +11,58 @@ </div> <p> These tracks show the genomic positions of variants in the <a href="https://www.ncbi.nlm.nih.gov/clinvar/" target="_blank">ClinVar database</a>. ClinVar is a free, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. </p> <p> The <b>ClinVar CNVs track</b> displays copy number variants (CNVs) equal or larger than 50 bp, and the <b>ClinVar SNVs track</b> displays substitutions and indels shorter than 50 bp. Until October 2017, all variants with the ClinVar types <em>copy number gain/loss</em> and <em>DbVar "nsv" accessions</em> were assigned in the CNV -category. Because the ClinVar type no longer captures this information, any variation equal or +category. Because the ClinVar type no longer captures this information, any variation equal to or larger than 50 bp is now considered a CNV. </p> <p> <b>Note:</b> The data in the track are obtained directly from ClinVar's FTP site. We display the data obtained from ClinVar as-is to avoid discrepancies between UCSC and NCBI. However, be aware that the ClinVar conventions are different from the VCF standard. Variants may be right-aligned or may contain additional context, e.g. for inserts. ExAC/gnomAD make available <a href="https://github.com/macarthur-lab/clinvar" target="_blank">a converter</a> to make ClinVar more comparable to VCF files.</p> <h2>Display Conventions and Configuration</h2> <p> The genomic locations of ClinVar variants are labelled with the ClinVar variant descriptions. <b>Mouseover</b> on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. </p> <p> Entries in the <b>ClinVar CNV track</b> are colored by <b>type of variant</b>: <b><font color="da2c37">red for loss</font></b>, <b><font color="294eae">blue for gain</font></b>, and <b><font color="840876">purple for insertion</font></b>. -A light to dark color gradient indicates the clinical significance of each variant, with the -lightest shade being benign, or others, to the darkest shade being pathogenic. +A light-to-dark color gradient indicates the clinical significance of each variant, with the +lightest shade being benign, to the darkest shade being pathogenic. </p> <p> Entries in the <b>ClinVar SNVs track</b> are colored by <b>clinical significance</b>: <b><font color="d20000">red for pathogenic</font></b>, <b><font color="000088">dark blue for variant of uncertain significance</font></b>, <B><font color="#00d200">green for benign</font></b>, <B><font color="#888">dark grey for not provided</font></b>, and <B><font color="#8979D4">light blue for conflicting</font></b>. </p> <p> Items can be filtered according to the size of the variant, variant type, clinical significance, allele origin, and molecular consequence, using the track <b>Configure</b> options. Each subtrack has separate display controls, as described