ef238e6ab90d807a28fc144fa520b50c0d1b9801 mspeir Mon Nov 3 17:12:17 2025 -0800 changing genome-source to github references, refs #35031 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 031ac37915a..21e779e75c7 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -9461,33 +9461,33 @@ ingestion pipeline. Below is a short summary of the UCSC changes brought forth by both dbSNP's redesign, as well as UCSC's new pipeline.</p> <ul> <li>New track type bigDbSnp</li> <li>Expanded dbSNP track composition</li> <li>New UCSC annotation of dbSNP data termed <b>UCSC Notes</b></li> <li>dbSNP data will now be a bigBed file download (see Data Access below)</li> </ul> <h3>bigDbSnp and dbSNP v153</h3> <p> "SNPs" tracks were previously based on related mysql database tables, but the new bigDbSnp format is a bigBed file with extra columns that contains all necessary information to display the variant. An accompanying dbSnpDetails file contains additional data displayed in the item details page. Schemas are available for both <a target="_blank" -href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/bigDbSnp.as"> +href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/lib/bigDbSnp.as"> bigDbSnp</a> and <a target="_blank" -href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/dbSnpDetails.as"> +href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/lib/dbSnpDetails.as"> dbSnpDetails</a>.</p> <p> dbSNP's redesign includes an important change to the representation of insertion/deletion variants (indels) in repetitive regions. Rather than annotating the minimal representation of the indel on the genome, dbSNP now expands the reference and alternate alleles to cover the entire repetitive region on the genome. Accordingly, we display the newly expanded regions, but use thin and thick lines to indicate the region of uncertain placement and the minimal size. For example, when there is a deletion of one base in a range of three identical bases, we draw a thin rectangle over the first two bases to show that there is uncertain placement, and a thick rectangle over the last base to show that one base is deleted from the range. Some indel variants have multiple alternate alleles. You may notice some thick but gray rectangles when there are deletion alleles of different sizes.</p> <p> Below is an image from an <a target="_blank" href="https://genome.ucsc.edu/s/Lou/hg38DbSnpNews"> example session</a> which displays an instance of this new visualization. In a repetitive region