7072384d5e6f4228bec4186d3d677527be0c9bc5
mspeir
  Fri Jun 26 09:37:20 2026 -0700
Adding data access to hs1 pages on the RR, refs #

diff --git src/hg/makeDb/trackDb/human/hs1/problematic.html src/hg/makeDb/trackDb/human/hs1/problematic.html
index ab041f9b89a..b7ca2281e8f 100644
--- src/hg/makeDb/trackDb/human/hs1/problematic.html
+++ src/hg/makeDb/trackDb/human/hs1/problematic.html
@@ -10,30 +10,54 @@
 target="_blank">Genome in a Bottle (GIAB) consortium</a>, and the
 <a href="https://sites.google.com/ucsc.edu/t2tworkinggroup"
 target="_blank">Telomere-to-Telomere Consortium (T2T)</a>, the dataset aims to standardize the
 analysis of genetic variation by offering pre-defined BED files for stratifying true and false
 positives in genomic studies, facilitating accurate assessments in complex areas of the genome.</p>
 
 <h2>Methods</h2>
 <p>
 The creation of the GIAB Problematic Regions tracks involves using a pipeline and configuration to
 generate stratification BED files that categorize genomic regions based on specific challenges,
 such as low complexity or difficult mapping, to facilitate accurate benchmarking of variant calls.
 For more information on the pipeline and configuration used, please visit the following webpage:
 <a href="https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/README.md">
 https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/README.md</a>.</p>
 
+<h2>Data Access</h2>
+<p>
+The raw data can be explored interactively with the
+<a href="../cgi-bin/hgTables" target="_blank">Table Browser</a> or the
+<a href="../cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. The data can also be
+accessed from scripts through our <a href="https://api.genome.ucsc.edu" target="_blank">REST
+API</a>.</p>
+<p>
+This track is a container of multiple subtracks; the underlying data are stored in bigBed files
+that can be downloaded from our
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/problematic/GIAB/" target="_blank">download server</a>.
+Individual regions or the whole genome annotation can be obtained using our tool
+<tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled
+binary for your system. Instructions for downloading source code and binaries can be found
+<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.
+The tool can also be used to obtain only features within a given range, for example:</p>
+<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/problematic/GIAB/alldifficultregions.bb -chrom=chr6 -start=0 -end=1000000 stdout</tt>
+<p>
+Please refer to our
+<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing
+list archives</a> for questions, or our
+<a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more
+information.</p>
+
 <h2>Contact</h2>
 <p>If you have questions or comments, please write to Justin Zook (jzook@nist.gov).</p>
 
 <h2>References</h2>
 <p>
 Dwarshuis N, Kalra D, McDaniel J, Sanio P, Alvarez Jerez P, Jadhav B, Huang WE, Mondal R, Busby B,
 Olson ND <em>et al</em>.
 <a href="https://doi.org/10.1038/s41467-024-53260-y" target="_blank">
 The GIAB genomic stratifications resource for human reference genomes</a>.
 <em>Nat Commun</em>. 2024 Oct 19;15(1):9029.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39424793" target="_blank">39424793</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11489684/" target="_blank">PMC11489684</a>
 </p>
 
 Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA,