-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 vg deconstruct and -decomposed into atomic alleles with vcfwave (WFA2-lib). -
--The hg38 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. 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. -
- --Items are colored by SV type: -
-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). -
- --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 vg deconstruct and then decomposed into atomic -alleles with vcfwave / 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| ≥ 50 bp or the INV 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 - -hprc_intermediate_assembly/alignments_v2.0.csv. -
--The HPRC v2.0 Minigraph-Cactus graph and wave-decomposed VCFs were -downloaded from the HPRC S3 release bucket: - -hprc-v2.0-mc-grch38.wave.vcf.gz (hg38) and - -hprc-v2.0-mc-chm13.wave.vcf.gz (hs1). -
--The step-by-step build commands (download, format conversion, bigBed build) -are recorded in the UCSC makeDoc for this track container: - -doc/hg38/lrSv.txt and - -doc/hs1/lrSv.txt. The conversion scripts and autoSql schemas live in - -makeDb/scripts/lrSv. -
- --The data can be explored interactively in table format with the -Table Browser or the -Data Integrator, and accessed -programmatically through our API, -track=hprc2Sv. -
--The bigBed is available from our download server for both assemblies: -
-The original pangenome graph and the wave-decomposed VCF are available -from the HPRC public S3 bucket, as linked from the -HPRC -release-2 announcement. -
- --Thanks to the Human Pangenome Reference Consortium for building and -publicly releasing the release-2 minigraph-cactus pangenome. -
- --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: - -HPRC data release 2. -