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/hprc2Sv.html src/hg/makeDb/trackDb/human/hprc2Sv.html
deleted file mode 100644
index 11a002d914b..00000000000
--- src/hg/makeDb/trackDb/human/hprc2Sv.html
+++ /dev/null
@@ -1,118 +0,0 @@
-<h2>Description</h2>
-<p>
-This track shows structural variants (SVs) derived from the Human Pangenome
-Reference Consortium (HPRC) release-2 pangenome graph. The graph was built
-with minigraph-cactus from PacBio HiFi haplotype-resolved assemblies of 233
-samples (including T2T-CHM13 and the diverse 1000 Genomes Project sample
-set). HPRC releases one VCF per reference path (GRCh38 and T2T-CHM13);
-we display both natively on the corresponding UCSC assembly (hg38 and hs1).
-Variants were extracted from the graph with <tt>vg deconstruct</tt> and
-decomposed into atomic alleles with <tt>vcfwave</tt> (WFA2-lib).
-</p>
-<p>
-The hg38 track contains 1,483,114 SV-sized alleles (length &ge; 50 bp) split
-by type: 1,106,190 insertions, 192,597 deletions, 178,178 complex alleles
-and 6,149 inversions. The hs1 track is built from the parallel T2T-CHM13
-wave VCF. Each row carries the allele count, allele frequency, number of
-samples with data and the snarl-nesting level of the variant in the
-pangenome decomposition tree.
-</p>
-
-<h2>Display Conventions and Configuration</h2>
-<p>
-Items are colored by SV type:
-<ul>
-<li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li>
-<li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li>
-<li><span style="color: rgb(140,0,200);">Complex alleles (COMPLEX)</span> - purple</li>
-<li><span style="color: rgb(230,140,0);">Inversions (INV)</span> - orange</li>
-</ul>
-</p>
-<p>
-Insertions are placed at the insertion site with a width of 1 bp; deletions,
-complex alleles and inversions span the affected reference interval.
-Filters are available for SV type, SV length, allele frequency and snarl
-level (0 = top-level bubble; higher values are nested within parent
-bubbles).
-</p>
-
-<h2>Methods</h2>
-<p>
-HPRC release-2 is an open data release (not yet accompanied by a formal
-peer-reviewed publication) built from PacBio HiFi haplotype-resolved
-assemblies of 233 samples, including T2T-CHM13 and a diverse 1000 Genomes
-Project panel. The pangenome graph was built with Minigraph-Cactus against
-both GRCh38 and T2T-CHM13 reference paths; variants were extracted from
-the graph with <tt>vg deconstruct</tt> and then decomposed into atomic
-alleles with <tt>vcfwave</tt> / WFA2-lib, yielding per-allele TYPE and LEN
-fields. For this track, each ALT in the wave VCF was emitted as its own
-BED row, retaining alleles with |LEN| &ge; 50 bp or the <tt>INV</tt> flag;
-allele counts, frequencies, sample counts and snarl levels are taken
-directly from the per-allele INFO fields. On hg38 this yields 1,483,114
-SV-sized alleles (1,106,190 insertions, 192,597 deletions, 178,178 complex
-alleles and 6,149 inversions); the hs1 track is built from the parallel
-T2T-CHM13 wave VCF. Sample-list and assembly provenance for the graph are
-maintained at HPRC in
-<a href="https://github.com/human-pangenomics/hprc_intermediate_assembly/blob/main/data_tables/pangenomes/alignments_v2.0.csv" target="_blank">
-hprc_intermediate_assembly/<tt>alignments_v2.0.csv</tt></a>.
-</p>
-<p>
-The HPRC v2.0 Minigraph-Cactus graph and wave-decomposed VCFs were
-downloaded from the HPRC S3 release bucket:
-<a href="https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/hprc-v2.0-mc-grch38.wave.vcf.gz" target="_blank">
-hprc-v2.0-mc-grch38.wave.vcf.gz</a> (hg38) and
-<a href="https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/hprc-v2.0-mc-chm13.wave.vcf.gz" target="_blank">
-hprc-v2.0-mc-chm13.wave.vcf.gz</a> (hs1).
-</p>
-<p>
-The step-by-step build commands (download, format conversion, 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> and
-<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hs1/lrSv.txt" target="_blank">
-doc/hs1/lrSv.txt</a>. The conversion scripts and autoSql schemas live in
-<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank">
-makeDb/scripts/lrSv</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>hprc2Sv</i>.
-</p>
-<p>
-The bigBed is available from our download server for both assemblies:
-<ul>
-<li>GRCh38:
-<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/hprc2.bb" target="_blank">
-hg38 hprc2.bb</a></li>
-<li>T2T-CHM13:
-<a href="http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/hprc2.bb" target="_blank">
-hs1 hprc2.bb</a></li>
-</ul>
-Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/hprc2.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>.
-</p>
-<p>
-The original pangenome graph and the wave-decomposed VCF are available
-from the HPRC public S3 bucket, as linked from the
-<a href="https://humanpangenome.org/hprc-data-release-2/" target="_blank">HPRC
-release-2 announcement</a>.
-</p>
-
-<h2>Credits</h2>
-<p>
-Thanks to the Human Pangenome Reference Consortium for building and
-publicly releasing the release-2 minigraph-cactus pangenome.
-</p>
-
-<h2>References</h2>
-<p>
-HPRC release-2 data is not yet described in a formal peer-reviewed
-publication. See the Human Pangenome Project release announcement
-for background and data-access details:
-<a href="https://humanpangenome.org/hprc-data-release-2/" target="_blank">
-HPRC data release 2</a>.
-</p>