0871110b9e07cfb8001e6de9d156e7e7f74f8c25 max Fri Sep 4 17:00:53 2026 -0700 STRchive track now updates itself, and is on hg19 and hs1 as well as hg38 STRchive builds a Genome Browser bigBed with every release now and publishes it on their GitHub releases page, so there is nothing left for us to convert. A new otto job checks weekly for a new release, downloads the file into its own releases/<tag> directory, sanity-checks the locus count, and repoints the /gbdb symlinks at it. Silent when there is no new release. See STRchive issue 333 for the correspondence that set this up. Their releases carry hg19, hg38 and T2T-chm13 (= hs1) files and we take all three, so the new strVar stanza lives in human/strVarNew.ra rather than under hg38. The bigDataUrls use $D, and hgTrackDb -strict drops any member whose file is missing, so each assembly gets only the tracks that were built for it: STRchive on all three, the other four on hg38 only. The description page is rewritten for the new evidence-level coloring, gains an evidence filter, and now says that the track updates itself and that older versions are on GitHub rather than here. All of that is alpha only. Nothing copies /gbdb/*/strVar/ out to the RR yet, so releasing this trackDb would have it promise data the RR does not have. The old hg38-only version stays as human/hg38/strVar.ra, tagged beta,public, until the sysadmins install the strchiveAutoPush cron drafted alongside the otto job. The header of strVarNew.ra lists what to delete and rename then. refs #38268 diff --git src/hg/makeDb/trackDb/human/strVarNew.html src/hg/makeDb/trackDb/human/strVarNew.html new file mode 100644 index 00000000000..185c29e3d4c --- /dev/null +++ src/hg/makeDb/trackDb/human/strVarNew.html @@ -0,0 +1,56 @@ +<h2>Description</h2> +<p> +Tandem repeats are among the most polymorphic loci in the genome due to high +rates of repeat unit insertions and deletions caused primarily by polymerase slippage +during DNA replication. +The <b>Tandem Repeat Variation</b> track contains a collection of tracks +displaying population-level genetic variation at tandem repeat loci across +the human genome. Short tandem repeats (STRs), also known as +microsatellites, are consecutive repetitions of 1-6 nucleotide motifs. +Variable Number Tandem Repeats (VNTRs) are tandem repeats of typically +7-100 bp. +</p> + +<p> +This super track provides genome-wide tandem repeat annotations, allele frequency data from +large-scale population cohorts, and curated disease-associated STR loci.</p> + +<p>Note that the gnomAD track container also includes an STR variation track, which is not part +of the container here.</p> + +<h2>Tracks in this collection</h2> +<p> +Not every track is available on every assembly. The list below covers the whole +collection; the track configuration page for this assembly shows the ones you can +actually turn on here. STRchive is on hg19, hg38 and hs1 (T2T-CHM13); the rest are +hg38 only.</p> +<ul> +<li><b><a href="hgTrackUi?g=webstr">WebSTR</a></b> (hg38 only) — +1.7 million STR loci from the EnsembleTR panel with allele frequency data from the +1000 Genomes Project (3,550 individuals across five continental populations). +See the <a href="hgTrackUi?g=webstr">WebSTR track documentation</a> for full details.</li> +<li><b><a href="hgTrackUi?g=trexplorer">TRExplorer</a></b> (hg38 only) — +5.6 million tandem repeat loci (STRs and VNTRs) from the +TRExplorer catalog at the Broad Institute, with population allele +frequency data from TenK10K, HPRC256, and AoU1027 cohorts. +See the <a href="hgTrackUi?g=trexplorer">TRExplorer track documentation</a> for full details.</li> +<li><b><a href="hgTrackUi?g=strchive">STRchive</a></b> (hg19, hg38, hs1) — +disease-associated tandem repeat loci curated from published literature, with +pathogenic repeat thresholds, inheritance modes, and disease annotations. +See the <a href="hgTrackUi?g=strchive">STRchive track documentation</a> for full details.</li> +<li><b><a href="hgTrackUi?g=tommoStr">ToMMo 61K STR</a></b> (hg38 only) — +174,300 STR loci with allele count distributions from 61,000 Japanese individuals +(Tohoku Medical Megabank Organization), genotyped with Expansion Hunter. +See the <a href="hgTrackUi?g=tommoStr">ToMMo STR track documentation</a> for full details.</li> +<li><b><a href="hgTrackUi?g=viennaVntr">1KG Vienna ONT VNTR</a></b> (hg38 only) — +361,362 VNTR loci with allele statistics from 1,019 samples of the 1000 Genomes +Oxford Nanopore long-read sequencing project (Vienna), genotyped with VAMOS. +Unlike the other STR tracks which use short-read data, this track is based on +long-read sequencing which can span longer tandem repeat regions. +See the <a href="hgTrackUi?g=viennaVntr">Vienna VNTR track documentation</a> for full details.</li> +</ul> + +<h2>Credits</h2> +<p> +Thanks to the data providers of the individual tracks listed above. +See each track's documentation page for specific credits.</p>