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/html/gwasSNPs2022-03-08.html src/hg/makeDb/trackDb/human/hs1/html/gwasSNPs2022-03-08.html
index 95f64d14eb8..0a4548c6f54 100644
--- src/hg/makeDb/trackDb/human/hs1/html/gwasSNPs2022-03-08.html
+++ src/hg/makeDb/trackDb/human/hs1/html/gwasSNPs2022-03-08.html
@@ -1,14 +1,32 @@
 <h2>Description</h2>
 <p>A GWAS Catalog VCF was generated by intersecting RefSeq IDs in the GWAS Catalog associations v1.0 file (ebi.ac.uk/gwas/api/search/downloads/full, accessed 2022-03-08) with all dbSNP build 155 variants on the primary contigs for Chromosomes 1-22, Chromsome X and Chromosome Y. These variants were lifted over from GRCh38 to the T2T-CHM13 assembly. This track contains GWAS Catalog variants that lifted over from GRCh38 to the T2T-CHM13v2.0 assembly. This includes variants that lifted over perfectly, as well as variants that failed initial liftover due to reference/alternative allele swaps but were recovered on subsequent liftover, with reference and alternative alleles swapped appropriately.</br></br>
 These two sets of variants are included together in this track. If you are interested in downloading these sets separately (i.e., variants that lifted over perfectly vs. recovered variants with ref/alt allele swaps) they can be accessed here: <a href="https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/annotation/liftover/">https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/annotation/liftover/</a>.</p>
 
 <h2>Methods</h2>
 <p>We performed liftover using the GATK release 4.1.9 LiftoverVcf (Picard Version 2.23.3) tool with the default parameters. This successfully lifts over variants that map exactly from GRCh38 to T2T-CHM13v2.0 but does not recover variants with swapped reference and alternative alleles. To recover variants with swapped reference/alternative alleles, we ran LiftoverVCF again, with the <code>RECOVER_SWAPPED_REF_ALT</code> flag. Notably, this feature does not recover multiallelic variants, so to recover these variants, we first separated them into multiple biallelic variants, performed liftover using the <code>RECOVER_SWAPPED_REF_ALT</code> tag, and converted them back to their multiallelic representations.</p>
 
+<h2>Data Access</h2>
+<p>
+The variant 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>, where the track name is <tt>gwasSNPs2022-03-08</tt>.</p>
+<p>
+The underlying VCF file is available from our
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/gwasSNPs2022-03-08/" target="_blank">download server</a> as
+<tt>chm13v2.0_GWASv1.0rsids_e100_r2022-03-08.vcf.gz</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>Contacts</h2>
 <ul>
   <li><a href="mailto:dtaylo95@jhu.edu">Dylan Taylor &lt;dtaylo95 at jhu.edu&gt;</a>
   <li><a href="mailto:rmccoy22@jhu.edu">Rajiv McCoy &lt;rmccoy22 at jhu.edu&gt;</a>
 </ul>
 <h2>References</h2>
 <p>Van der Auwera GA & O'Connor BD. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (1st Edition). O'Reilly Media.</p>