23f68df8fb0481fd1bd4351f4adbf913f039f237
max
  Mon Jul 20 11:49:57 2026 -0700
lrSv1kLin: add per-population AF filter defaults and full Data Access section

Add missing filter.afAfr/afAmr/afEas/afEur/afSas default ranges so the
per-population allele-frequency filters render. Expand the description page's
Data Access section to the standard form with bigBed download URLs for both
the hg38 and hs1 native builds. refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv1kLin.html src/hg/makeDb/trackDb/human/lrSv1kLin.html
index 9b819296a36..05b20758df6 100644
--- src/hg/makeDb/trackDb/human/lrSv1kLin.html
+++ src/hg/makeDb/trackDb/human/lrSv1kLin.html
@@ -69,27 +69,46 @@
 The data was provided by the laboratories of Evan Eichler and Danny Miller
 (University of Washington) and is preliminary and unpublished; a manuscript
 is in preparation. The step-by-step build commands (format conversion and
 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 script and autoSql schema live in
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank">
 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>
 The data can be explored interactively in table format with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the
-<a href="../cgi-bin/hgIntegrator">Data Integrator</a>, and accessed
-programmatically through our <a href="https://api.genome.ucsc.edu">API</a>,
-track=<i>lrSv1kLin</i>.
+<a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there
+to spreadsheet or tab-separated tables. From scripts, the data can be accessed
+through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>lrSv1kLin</i>.
+</p>
+<p>
+For automated download and analysis, the annotation is stored in bigBed files
+that can be downloaded from our download server:
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/lin1218.bb" target="_blank">
+http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/lin1218.bb</a> (GRCh38/hg38,
+native) and
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/lin1218.bb" target="_blank">
+http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/lin1218.bb</a> (T2T-CHM13/hs1,
+native). Individual regions or the whole annotation can be obtained with the
+<tt>bigBedToBed</tt> utility, which can be compiled from source or downloaded
+as a precompiled binary from our
+<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">utilities
+page</a>. The tool can also extract features within a given range, for example:
+<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/lin1218.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>.
+</p>
+<p>
+This is a preliminary, unpublished callset provided by the authors; the
+underlying per-sample sequencing data is not yet publicly released.
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to Evan Eichler, Danny Miller and colleagues at the University of
 Washington, and to the contributing 1000 Genomes long-read consortia (HPRC,
 HGSVC and the 1000 Genomes ONT sequencing groups), for generating and sharing
 this callset.
 </p>