01e223245a85e1ae6d1f2e914c64367cfd006ea9 ccpowell Tue Jul 9 16:00:29 2019 -0700 Changing MySQL to MariaDB in documentation, refs #23597 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 588e44a..6dc2547 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,31 +52,31 @@ <a name="2019"></a> <a name="070119"></a> <h2>Jul. 1, 2019   New DGV Gold Standard track for human (GRCh19/hg19)</h2> <p> We are pleased to announce the DGV Gold Standard track for human (GRCh19/hg19). This track displays copy number variants (CNVs), insertions/deletions (InDels), inversions and inversion breakpoints annotated by the <a href="http://dgv.tcag.ca/dgv/app/home" target="_blank">Database of Genomic Variants</a> (DGV). The initial criteria for the Gold Standard set require that a variant be found in at least two different studies and found in at least two different samples. After filtering out low-quality variants, the remaining variants are clustered according to 50% minimum overlap, and then merged into a single record. Gains and losses are merged separately. </p> <p> -The <a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=dgvPlus" target="_blank">DGV Gold Standard track</a> +The <a href="../cgi-bin/hgTrackUi?db=hg19&g=dgvPlus" target="_blank">DGV Gold Standard track</a> utilizes a boxplot-like display to represent the merging of records. The highest ranking variant in the cluster defines the inner "box", while the outer lines define the outermost start and stop coordinates of the CNV. In this way, the inner box forms a high-confidence CNV location and the thin connecting lines indicate confidence intervals for the location of the CNV. </p> <p class="text-center"> <img class='text-center' src="../images/dgvGold.png" width='850' alt="DGV Gold Standard track"> </p> <p> We would like to thank Jeff MacDonald and the <a href="http://dgv.tcag.ca/dgv/app/home" target="_blank">Database of Genomic Variants</a> group for providing guidance and these data. We would also like to thank Christopher Lee and Conner Powell as well as the entire UCSC Genome Browser team for creating and releasing this track. </p>