9a11061ca6b40fe16bdfd09b1af53192f6c7c85b max Tue Apr 21 08:13:02 2026 -0700 lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/hprc2Sv.html src/hg/makeDb/trackDb/human/hprc2Sv.html new file mode 100644 index 00000000000..5c3e89e4d93 --- /dev/null +++ src/hg/makeDb/trackDb/human/hprc2Sv.html @@ -0,0 +1,96 @@ +<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), aligned to the GRCh38 reference path. 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 track contains 1,483,114 SV-sized alleles (length ≥ 50 bp) split by +type: 1,106,190 insertions, 192,597 deletions, 178,178 complex alleles and +6,149 inversions. 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> +The HPRC v2.0 minigraph-cactus pangenome was downloaded as +<tt>hprc-v2.0-mc-grch38.sv.gfa.gz</tt> (the graph) and +<tt>hprc-v2.0-mc-grch38.wave.vcf.gz</tt> (the corresponding +wave-decomposed VCF) from the HPRC S3 release bucket. The VCF is the +result of running <tt>vg deconstruct</tt> on the graph with GRCh38 as the +reference path and then <tt>vcfwave</tt> / WFA2-lib to split complex +multi-allelic records into atomic alleles with per-allele TYPE and LEN +fields. +</p> +<p> +For display here, the wave VCF was streamed and each ALT was emitted as +its own BED row. Alleles were retained if their absolute length was +≥ 50 bp or if the record carried the <tt>INV</tt> flag (inversions may +be shorter). Allele counts, frequencies, and sample counts are taken +directly from the per-allele INFO fields. +</p> +<p> +The list of assemblies underlying the pangenome is documented at +<a href="https://github.com/human-pangenomics/hprc_intermediate_assembly/blob/main/data_tables/pangenomes/alignments_v2.0.csv" + target="_blank">human-pangenomics/hprc_intermediate_assembly +<tt>alignments_v2.0.csv</tt></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 +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our +download server</a> as <tt>hprc2.bb</tt>. 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>