ef61e73fc416622d8557ec2439df2344a1cc80c3
max
  Tue Jun 9 15:10:01 2026 -0700
lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv)

Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from
the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both
hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The
v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL
by parsimony-trimming REF/ALT and the net length change. The v2.0 build
recipe, converter and schema are kept but commented out in the makeDocs in
case wave-decomposed VCFs are released again, refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html
index c9c68e0f0a9..7d5560c1eac 100644
--- src/hg/makeDb/trackDb/human/lrSv.html
+++ src/hg/makeDb/trackDb/human/lrSv.html
@@ -127,39 +127,39 @@
   <td>186</td>
   <td>809,711</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=decodeSv">deCODE 3,622</a></td>
   <td>3,622</td>
   <td>Icelandic general population</td>
   <td>No</td>
   <td>~17x ONT</td>
   <td>133,886</td>
   <td>0</td>
   <td>127</td>
   <td>861,080</td>
 </tr>
 <tr>
-  <td><a href="hgTrackUi?g=hprc2Sv">HPRC v2</a></td>
+  <td><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1</a></td>
   <td>233</td>
   <td>HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies)</td>
   <td>No</td>
   <td>~60x HiFi + ~30x ONT (pangenome graph)</td>
-  <td>1,483,114</td>
+  <td>596,063</td>
   <td>50</td>
-  <td>280</td>
-  <td>97,718</td>
+  <td>276</td>
+  <td>1,064,897</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2</a></td>
   <td>32</td>
   <td>HGSVC2 haplotype-resolved assemblies (5 superpopulations)</td>
   <td>No</td>
   <td>&gt;40x PacBio CLR + &gt;20x HiFi (+ Strand-seq)</td>
   <td>111,746</td>
   <td>50</td>
   <td>168</td>
   <td>57,207,414</td>
 </tr>
 <tr>
   <td><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a></td>
   <td>65</td>
@@ -284,37 +284,37 @@
 replicated SVs (deletions, insertions, duplications, inversions) called with
 pbsv and merged with JASMINE. The matched GA4K small-variant callset (SNVs
 and short indels) lives alongside other population allele-frequency resources
 as <a href="hgTrackUi?g=ga4kSnv">GA4K 552 PacBio LR</a> in the Variant
 Frequencies track collection.
 </p>
 
 <h3><a href="hgTrackUi?g=decodeSv">deCODE 3,622 SVs</a></h3>
 <p>
 High-confidence structural variants from 3,622 Icelanders (deCODE genetics),
 sequenced with Oxford Nanopore long reads. ~134k SVs (deletions, insertions
 and combined insertion/deletion events). Site-only callset with annotated
 surrounding tandem-repeat regions.
 </p>
 
-<h3><a href="hgTrackUi?g=hprc2Sv">HPRC v2 SVs</a></h3>
+<h3><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1 SVs</a></h3>
 <p>
 Structural variants derived from the Human Pangenome Reference Consortium
-release-2 minigraph-cactus pangenome graph, built from 233 PacBio HiFi
+release-2.1 minigraph-cactus pangenome graph, built from 233 PacBio HiFi
 haplotype-resolved assemblies (CHM13 + diverse 1000 Genomes samples).
-~1.5M SV-sized alleles (INS, DEL, COMPLEX, INV) extracted with
-<tt>vg deconstruct</tt> and decomposed with <tt>vcfwave</tt> (WFA2).
+About 596k SV-sized alleles (insertions and deletions) extracted from the
+graph with <tt>vg deconstruct</tt>.
 </p>
 
 <h3><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2 32 SVs</a></h3>
 <p>
 Structural variants from 32 haplotype-resolved diploid genomes (HGSVC2
 freeze 4, Ebert et al. 2021). ~112k SVs (deletions, insertions and
 inversions) called from phased de novo assemblies with PAV, with
 per-variant 1000 Genomes population allele frequencies (insertions and
 deletions) and rich structural/gene annotations. An earlier HGSVC release
 complementary to <a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a>.
 </p>
 
 <h3><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3 65 SVs</a></h3>
 <p>
 Structural variants from 65 diverse individuals sequenced and de novo