9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 lrnassar Mon Jun 29 14:21:07 2026 -0700 lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released). diff --git src/hg/makeDb/trackDb/human/lrSv1kgOnt.html src/hg/makeDb/trackDb/human/lrSv1kgOnt.html index fa8be24c6ae..1f0600eecfd 100644 --- src/hg/makeDb/trackDb/human/lrSv1kgOnt.html +++ src/hg/makeDb/trackDb/human/lrSv1kgOnt.html @@ -76,31 +76,31 @@ <p> The SVAN-annotated unphased VCF (<tt>final-vcf.unphased.SVAN_1.3.vcf.gz</tt>) was downloaded from <a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/release/v1.1/svan-annotation/" target="_blank"> the IGSR 1KG_ONT_VIENNA v1.1 SVAN-annotation directory</a>; allele counts were added from the companion shapeit5-phased-callset (<tt>shapeit5-phased-callset_final-vcf.phased.vcf.gz</tt>) in the same release tree. </p> <p> The step-by-step build commands (download, liftOver, format conversion, bigBed build) are recorded in the UCSC makeDoc for this track container: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank"> doc/hg38/lrSv.txt</a>. The conversion scripts and autoSql schemas live in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank"> -makeDb/scripts/lrSv</a>. +makeDb/scripts/lrSv</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/lrSv.ra" target="_blank">trackDb/human/lrSv.ra</a>. </p> <h2>Data Access</h2> <p> Source data is available from the <a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/" target="_blank">1000 Genomes ONT Vienna</a> data collection at IGSR. </p> <h2>Credits</h2> <p> Thanks to the 1000 Genomes ONT Vienna consortium for making their structural variant calls and SVAN annotations publicly available. </p>