40c7b6fb506ddde686cd56a976b8a07e46db775b max Tue Apr 21 08:19:46 2026 -0700 hprc2Sv: highlight alignments_v2.0.csv as authoritative file list Reframe the existing link to HPRC's alignments_v2.0.csv in the Methods section so it is clear that this CSV points to both the GRCh38 and CHM13 pangenome VCFs used for the track (not just the list of underlying assemblies). Existing S3 download links preserved. refs #36258 diff --git src/hg/makeDb/trackDb/human/hprc2Sv.html src/hg/makeDb/trackDb/human/hprc2Sv.html index 5c3e89e4d93..ac1ba979642 100644 --- src/hg/makeDb/trackDb/human/hprc2Sv.html +++ src/hg/makeDb/trackDb/human/hprc2Sv.html @@ -1,96 +1,111 @@ <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). +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 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. +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. </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. +The HPRC v2.0 minigraph-cactus pangenome was downloaded from the HPRC S3 +release bucket: +<ul> +<li>hg38: +<a href="https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/hprc-v2.0-mc-grch38.sv.gfa.gz" target="_blank"><tt>hprc-v2.0-mc-grch38.sv.gfa.gz</tt></a> (graph) and +<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"><tt>hprc-v2.0-mc-grch38.wave.vcf.gz</tt></a> (wave-decomposed VCF)</li> +<li>hs1: +<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"><tt>hprc-v2.0-mc-chm13.wave.vcf.gz</tt></a></li> +</ul> +The VCF is the result of running <tt>vg deconstruct</tt> on the graph with +the corresponding reference path (GRCh38 or T2T-CHM13) 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 pointer to both the GRCh38 and CHM13 pangenome files (and the list of +assemblies that went into the graph) is maintained by HPRC 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>. +<tt>alignments_v2.0.csv</tt></a>, which links to both the hg38 and +CHM13/hs1 VCFs (and the underlying graph files) used for this track. </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>. +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>